Integrative biodiversity discovery: an introduction to field collection, laboratory analysis, and phylogenomics

Societal issues including the biodiversity crisis, zoonotic diseases, and climate change demand a precise understanding of what species are and where they fit on the tree of life. Biodiversity scientists are at the forefront of efforts to describe species and the organismal characteristics that make them relevant in our changing world. Unlocking the patterns of biodiversity requires modern tools including large-scale genomic data and technically rigorous analyses, but also practical knowledge of how to obtain samples from field research. The challenge addressed: While evolutionary relationships underpin the work of almost every environmental scientist, current training opportunities in biodiversity discovery (fieldwork) and interpretation (i.e., taxonomy, phylogenetics, and systematic biology) are few for postgraduate students. Aims and objectives: This training short course (TSC) will fill a pedagogical gap by providing an immersive introduction to integrative biodiversity discovery. From field to analysis, academic staff at the Natural History Museum will take course participants on a learning journey through current protocols and topics within systematic biology. Caretakers of one of the largest and oldest collections of environmental samples in the world, lecturers will share extensive expertise across three modules of biodiversity discovery: field collection, laboratory analyses, and powerful digital analyses. Attendees will learn the integrative skills necessary to link these three modules of biodiversity discovery at London’s Natural History Museum: an inspirational backdrop for training. Applications and benefits: Over a five-day course, twenty students from around the UK will be provided with a comprehensive introduction to biodiversity discovery and interpretation. A module on field collecting of a wide range of organisms (including those found in remote field sites) will introduce attendees to data curation, archiving, and ethical considerations. Next, students will learn how the chain of data custody is linked from field to the molecular laboratory. The NHM’s own molecular laboratory facility will provide lectures and practicals as an introduction to the short and long-read DNA sequencing methods that are used in integrative biodiversity discovery. Finally, an analytical module with lectures and practicals will guide students through phylogenomic methods including maximum likelihood inference and Bayesian coalescent analyses. From viruses to whales, phylogenomics has emerged as a powerful approach for inferring evolutionary relationships amongst organisms. Information obtained from these tree-building analyses informs not only how we name and study different species, but also how we understand interactions amongst ecological communities. Collectively, the TSC will increase biodiversity literacy and comprehension in a diverse group of early career scientists. The skills provided by this TSC support NERC’s Digital Strategy 2021 to 2030 in covering the dimensions of data stewardship (digital data collection in the field), data analysis (genomic sequencing in the lab), and modelling and simulation (phylogenomic analyses to reconstruct evolutionary histories). This training opportunity will also prepare students to meet the thematic challenges set out by UKRI in their strategy 2022 to 2027, as biodiversity literacy underpins building a green future (documenting and conserving biodiversity), securing a more resilient world (through biodiversity knowledge), creating opportunities across the UK (increasing biodiversity awareness in the emerging job force), better human wellbeing (improved livelihoods with biodiversity appreciation), and tackling infections (elucidating microbial and parasite diversity).