University of Oxford – Wytham Woods

Oxford

Who we are:

The University of Oxford is one of the oldest Universities in the world, and internationally recognized for teaching and research. In the biological sciences, we have been undertaking research into ecology and evolution for over 150 years, helping to lay the foundations for these subjects in collaboration with many others. Although our research activity spans the globe, for the Darwin Tree of Life project we are keeping our focus close to home. Just outside Oxford lies a large area of ancient semi-natural woodland that has been owned and maintained by the University since 1942. This beautiful and diverse 400-hectare site, known as Wytham Woods, has been used as a site for intensive research into biodiversity ever since. Our team includes ecologists, molecular biologists, bioinformaticians and specialists in education and outreach, who work together to bring the biological diversity of Wytham Woods to the Darwin Tree of Life project.

What we’re doing in the Darwin Tree of Life Project:

Our role in the Darwin Tree of Life project is as a Genome Acquisition Laboratory (GAL). The biological diversity of Wytham Woods has been well studied for decades, so we already know that the site holds a vast diversity of animal, plant, fungal and microbial species, although even today we do not have a full list of species present. We are collecting 1000s of specimens from Wytham Woods, carefully identifying and recording them, and processing them for DNA extraction. In the first phase of the Darwin Tree of Life, we are focussing attention on key groups of ecological, evolutionary and wider interest, including moths, hoverflies, beetles and bees, and our taxonomic span will grow as the project proceeds. In doing this, we have discovered many additional species present in the Woods that had never been recorded there before.

By focussing on one (albeit large) site, the sampling process is greatly simplified because we have equipped two laboratories  – one right in the heart of woods and one just outside – where we can process samples within hours, minutes or even seconds of collection. Furthermore, focussing on one site streamlines compliance with ethical and legal issues necessary for collection.

In this project our team does more than collect samples. Identification and recording requires expert skills, and becomes even more tricky as more and more species are collected. In addition, we coordinate and engage members of the public and expert amateurs in collecting and specimen identification tasks, ensuring a mutual flow of information and learning. We also use emerging data from the Darwin Tree of Life project in education: training undergraduate students in methods to handle and study DNA sequences. And we are involved in data analysis, taking genome sequence from the production and assembly partners in the project and analysing these for features in the genome that could relate to the biology of particular species. In this way we help ‘complete the circle’ – from collection to biological understanding.

Why we’re invested in the Darwin Tree of Life Project:

We believe there is a huge amount to be learnt from genome sequence data- not only from the specimens we collect in Wytham Woods, but from all around the GALs.  First, these sequences will become key reference genomes for ecological and environmental studies through the 21st century. Our fauna and flora are under threat due to land use change, invasive species, climate change and pathogen outbreaks. Understanding and predicting these changes, and possibly mitigating some of them, will require us to understand how each species responds to challenges at a cellular and molecular level. Such studies, including transcriptomic and proteomic analyses, will be greatly aided by reference genomes. Populations could also become fragmented or merged, and to detect these issues comparisons need to be made between individuals, something that will be facilitated by reference genomes. The second reason centres on evolution. Natural selection has adapted organisms to their environment through fixation of genetic change, and so hidden in the genome sequences will be clues to how evolution has shaped physiology, anatomy, life history, behaviour and other traits. There will surely be new genes, divergent sequences, genome duplications, horizontal gene transfers and much more: a deeper understanding of biodiversity is waiting to be discovered in Wytham Woods.