Advances in sequencing technologies and declining costs are increasing the accessibility of large-scale biodiversity genomic datasets. To maximise the impact of these data, a careful, considered approach to data management is essential. However, challenges associated with the management of such datasets remain, exacerbated by uncertainty among the research community as to what constitutes best practices. As an interdisciplinary team with diverse data management experience, we recognise the growing need for guidance on comprehensive data management practices that minimise the risks of data loss, maximise efficiency for stand-alone projects, enhance opportunities for data reuse, facilitate Indigenous data sovereignty and uphold the FAIR and CARE Guiding Principles. Here, we describe four fictional personas reflecting user experiences with data management to identify data management challenges across the biodiversity genomics research ecosystem. We then use these personas to demonstrate realistic considerations, compromises, and actions for biodiversity genomic data management. We also launch the Biodiversity Genomics Data Management Hub (https://genomicsaotearoa.github.io/data-management-resources/), containing tips, tricks and resources to support biodiversity genomics researchers, especially those new to data management, in their journey towards best practice. The Hub also provides an opportunity for those biodiversity researchers whose expertise lies beyond genomics and are keen to advance their data management journey. We aim to support the biodiversity genomics community in embedding data management throughout the research lifecycle to maximise research impact and outcomes.

A recent Molecular Ecology editorial made a proactive statement of support for the “Nagoya Protocol” and the principle of benefit-sharing (Marden et al. 2020) by requiring authors to provide a “Data Accessibility and Benefit‐Sharing Statement” in their articles. Here, we encourage another step that enables Indigenous communities to provide their own definitions and aspirations for access and benefit-sharing alongside the author’s “Statement”. We invite the Molecular Ecology research community to use Biocultural-, Traditional Knowledge-, and Cultural Institution Notices to help Indigenous communities gain visibility within our research structures. Notices are one of the tools offered by the Biocultural Labels Initiative (part of the Local Contexts system) designed specifically for researchers and institutions. The Notices are highly visible, machine-readable icons that signal the Indigenous provenance of genetic resources, and rights of Indigenous communities to define the future use of genetic resources and derived benefits. The Notices invite collaboration with Indigenous communities and create spaces within our research systems for them to define the provenance, protocols, and permissions associated with genetic resources using Labels. Authors contributing to Molecular Ecology can apply Notices to their articles by providing the persistent unique identifier and an optional use-statement associated with the Notice in their “Data Accessibility and Benefit‐Sharing Statement”. In this way, our research community has an opportunity to accelerate support for the principles of the Nagoya Protocol, to alleviate concerns regarding Indigenous Data Sovereignty and equitable outcomes, and to build better relationships with Indigenous collaborators to enhance research, biodiversity, and conservation outcomes.

Classical taxonomic approaches to quantifying biodiversity can be notoriously laborious and restrictive. Instead, molecular metabarcoding is emerging as a rapid, high-throughput and cost-effective tool to catalogue biodiversity. Despite the appeal of metabarcoding however, methodological and procedural biases must be understood before robust biodiversity inferences can be made. Here, we use CO1 metabarcoding to characterize marine eukaryote communities associated with the holdfasts of Ecklonia radiata, the dominant eco-engineering kelp of temperate New Zealand and Australia. To establish a standardized and reproducible community metabarcoding protocol, we examined the influence of different sample preparation, laboratory and bioinformatic steps on inferences of species richness and composition for kelp-holdfast communities. Specifically, we examined: the effect of fractioning the community into different size classes, the replicability of results across DNA extractions, PCR reactions, and sequencing. Overall, our approach identified 18 marine eukaryote Phyla in the holdfast communities. We found that size fractioning the sample before DNA extraction enabled detection of a greater diversity of taxa, especially smaller organisms. When compared with traditional morphology-based inventories of kelp-holdfast biodiversity, we found that although the taxonomic precision of our metabarcoding approach at the species and genus level was limited by the availability of reference sequences in public repositories, we recovered a greater number of operational taxonomic units, and a greater taxonomic breadth of organisms than morphological surveys. Based on our findings, we provide methodological guidelines for the use of metabarcoding as a tool for surveying and monitoring the hyperdiverse species assemblages associated with kelp-holdfasts.

Classical taxonomic approaches to quantifying biodiversity can be notoriously laborious and restrictive. Instead, molecular metabarcoding is emerging as a rapid, high-throughput and cost-effective tool to catalogue biodiversity. Despite the appeal of metabarcoding however, methodological and procedural biases must be understood before robust biodiversity inferences can be made. Here, we use CO1 metabarcoding to characterize marine eukaryote communities associated with the holdfasts of Ecklonia radiata, the dominant eco-engineering kelp of temperate New Zealand and Australia. To establish a standardized and reproducible community metabarcoding protocol, we examined the influence of different sample preparation, laboratory and bioinformatic steps on inferences of species richness and composition for kelp-holdfast communities. Specifically, we examined: the effect of fractioning the community into different size classes, the replicability of results across DNA extractions, PCR reactions, and sequencing. Overall, our approach identified 18 marine eukaryote Phyla in the holdfast communities. We found that size fractioning the sample before DNA extraction enabled detection of a greater diversity of taxa, especially smaller organisms. When compared with traditional morphology-based inventories of kelp-holdfast biodiversity, we found that although the taxonomic precision of our metabarcoding approach at the species and genus level was limited by the availability of reference sequences in public repositories, we recovered a greater number of operational taxonomic units, and a greater taxonomic breadth of organisms than morphological surveys. Based on our findings, we provide methodological guidelines for the use of metabarcoding as a tool for surveying and monitoring the hyperdiverse species assemblages associated with kelp-holdfasts.