Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis

Abstract

High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.

Keywords: DNA metabarcoding; Genomic Observatories; biodiversity assessment; harmonized data generation; high-throughput sequencing.

FIGURE 1

Conceptual representation of the modular framework for harmonized data generation within a spatially led Genomic Observatories (GOs) network. (a) Representation of the three principal axes of the GO concept: space, time and genome. (b) Representation of the modular structure for protocol harmonization across GOs. Modules, as basic building blocks of the framework, can provide simple, integrated and interoperable procedures for site‐based characterization of extensive biodiversity fractions. Black block: module 1 (e.g., soil biodiversity); white block: module 2 (e.g., terrestrial arthropods); coloured blocks: protocols or submodules across the sequence of the five steps for a harmonized generation of inventory data within each module. (c) Map showing how modules can be implemented in: (c1) a spatially led network of sites for biodiversity inventory with shallow temporal and genomic efforts (spatial axis for the GO network concept); (c2) replicated through time within a site by repeated module implementation or historical samples (temporal axis for the SuperGO concept); and (c3) complemented with genomic resources (e.g., partial and complete genomes, microbiomes, gut contents) for specimens/assemblages within a site (genomic axis for the SuperGO concept)