NatureScot: Race is on to track down the tree of life

As we face this threat, we need to find ways to preserve the natural ecosystems that we have. An answer to these challenges is likely to be found in sequencing genomes – the sets of DNA present in all organisms.

An internationally important project to carry out this work is currently being undertaken in Scotland and across Britain and Ireland by a pioneering initiative known as the Darwin Tree of Life project.

Part of this game-changing science is being conducted at the Beinn Eighe National Nature Reserve in Wester Ross, managed by NatureScot, Scotland’s nature agency.

The hugely ambitious project will run until 2029 and aims to sequence, assemble and openly publish the genomes of all species found in Britain and Ireland, beginning with 2000 species representing every family of plant, animal and fungus.

It also aims to develop the tools and techniques that will be needed to complete the cataloguing of tens of thousands of remaining species before the end of the decade.

As well as NatureScot, a number of other highly respected organisations are involved in the project. They include the Royal Botanic Garden Edinburgh, the University of Edinburgh, the Natural History Museum in London and the Wellcome Sanger Institute’s Tree of Life programme.

In addition, experts from National Museums Scotland and the Highlands Biological Recording Group, a citizen science organisation which has been surveying Highland wildlife since the 1980s, have played an important role in the research in Scotland.

Professor Mark Blaxter is the Project Lead at the Wellcome Sanger Institute near Cambridge, one of the world’s leading genome research organisations. He said: “One of the goals of the project is that we will really start to understand the processes that generate biodiversity – the processes of evolution. It might let us predict what is going to happen in the future.”

David O’Brien, NatureScot’s Biodiversity Evidence and Reporting Manager says the scope and ambition of the project was a major draw for the agency: “When we first heard about this, we thought that this was potentially a game changer for genetic research in the UK and Ireland, but specifically so in Scotland.

“It’s an extremely ambitious project, but it has so many potential benefits when it comes to nature conservation. We tend to think of nature as either a habitat or a species – a woodland, for instance, or a Scots pine tree within that woodland.

“We don’t normally think about the genes within that tree, or within the woodpecker that’s banging on it. But genes are the building blocks for all of it. You can’t have species without these.”

Sample collecting from Beinn Eighe has already started. A recent trip in September focused on invertebrates, particularly wasps and moths, while earlier ones have concentrated on flora.

Techniques used in the field include sweeping, which involves catching flying insects in nets, and beating – in other words, knocking bugs, larvae and similar species out of the trees and onto canvas.

Another method is suction sampling, sometimes called bug hoovering. This involves the use of a machine that resembles a reverse leaf blower to suck invertebrates out of the undergrowth.

Other technologies used include a pooter – two rubber tubes attached to each other at either end of a sample container. By sucking on one end of the device, the collector can get specimens into a container with a high degree of accuracy. A gauze filter stops the specimen becoming an unwanted snack for the collector.

In addition, bright lamps are placed inside cylindrical traps. These attract moths overnight which are also then collected.

Once they have been gathered in, a small sample is identified by expert taxonomists before being flash frozen to preserve their DNA, which degrades very quickly after death. They are then transported to the Natural History Museum for DNA barcoding – an essential part of the process which looks at unique segments of each species' genome, which is a helpful way to then quickly identify them in their environments. Finally, samples are taken to Sanger for whole genome sequencing.

“We are seeing signs of biodiversity decline all around us”, says David O’Brien. “Obviously, we are worried. Those genetic building blocks hold the key to resilience and how animals, plants and fungi will adapt. So when the idea of this project was floated past me, I thought we just had to be part of it.”

NatureScot is deeply and actively involved in the study, helping to fund the laboratory work and having an input into the key species that will be sequenced first. It has also made its managed sites available – Beinn Eighe is the focal point, but lichens have been collected from its other reserves.

“We are making sure that everything goes smoothly by ensuring that everything is coordinated and that the various nature-related bodies can understand why we are doing this and what we hope to get from it. We will also get to use some of the information in the later stages of the project.”

There are a number of things that can be done with this data, Dr O’Brien says. “One use comes from collecting Environmental DNA (eDNA) through a technique that works best in ponds and rivers. We are already doing this in Scotland – we take water samples and put them through a filter in a lab.

“You then look at the DNA that is in the water, shed from skin or from the faeces, and that will indicate the species present. It’s really useful for knowing where they can be found and it reduces disturbance of them compared to other survey methods. That’s helpful when it comes to conservation.”

Climate change, he adds, means that new diseases and pathogens are arriving in Scotland. “Having genetic diversity will give the animals and plants more scope when it comes to having resistance, and sequencing will help us to understand this.

“Also, as climate change starts to affect our wildlife, we expect that some species will be better able to adapt, and within those species there will be individual examples that have the genes to help them cope a bit better with the new regime.

“If we are serious about protecting nature for its own sake as well as for the benefits we get from it, then making sure that we have the full toolbox is key. To have that, we need to understand what is there at a genetic level.”

Yet another benefit of the project is that genome sequencing can reveal that two species that look the same are in fact completely different. This means that it is possible that we discover species we do not currently know exist.

There is a tendency in Scotland, David O’Brien says, to believe that none have been lost here since the great auk became extinct in the 1840s. “But we could be losing some tiny creatures without even knowing they were ever there.

“However, if I was a betting man, I’d be happy to put a small wager on us discovering some new species through this project. In Scotland, we already have an international reputation for genetics in relation to wild species, and that’s something we can build on and share with other countries.”

Beinn Eighe is a treasure trove for harvesters of genomic data

Choosing a main survey area for the groundbreaking Darwin Tree of Life project proved to be a major challenge for the team involved – not because there were too few potential locations in Scotland, but because there were so many.

“When it came to choosing a focal site, we were faced with a tremendous task”, says David O’Brien. “So many are internationally recognised.”

In the end, Beinn Eighe in Wester Ross was thought to be particularly well qualified. It was the first national nature reserve to be established 70 years ago and is home to a wide variety of animals, fungi and plants.

These include the northern prongwort, a liverwort found nowhere else in the world apart from on a neighbouring mountain. Beinn Eighe was also the first Gene Conservation Unit to be registered in the UK in recognition of its work to protect the locally adapted Scots pine.

However, other sites in Scotland will also be surveyed. So far more than 150 specimens from over 100 different species have been collected. A highlight has been a moth, Griposia aprilina, also known as the merveille du jour or marvel of the day. It is perfectly adapted to camouflage itself against lichen.

The data gathered from the project are likely to prove hugely useful. Genomic data will help us to gain a fuller understanding of how species have evolved and responded to changes in climate.

This in turn will help humankind to address some of the fundamental problems it faces when it comes to land use, food production and decarbonisation.

The reference genome data will also prove to be a treasure trove for biotechnologists and pharmaceutical scientists looking for novel biomaterials – substances that have been engineered to interact with biological systems for a medical purpose.

The data will also be massively useful to medical researchers and benefit human health – for example, by helping to develop new antibiotics to overcome antimicrobial resistance or treatments, or for fighting emergent pathogens leading to illnesses such as Covid-19.

Biomaterials will also have an important role to play in creating a sustainable future and a post-carbon economy. They could prove to be key to scientific and technological development in a number of areas, including micro systems operating via sensory inputs and post-oil rubber and plastics.

“Genetic diversity underpins the adaptive potential of species and so the resilience of ecosystems”, says David O’Brien. “We became involved in this project because we recognise that if we are to safeguard this, we first need to understand it.

“We see it as a great opportunity to ensure the genetic diversity of Scotland’s wildlife is recorded and made available to all.”

‘IT IS GOING TO BE TRANSFORMATIVE’

Understanding and conserving biodiversity is fundamental to human survival and the Darwin Tree of Life project will advance our knowledge in this area, according to one of the leading figures working on the initiative.

Professor Mark Blaxter is the Project Lead at the Wellcome Sanger Institute near Cambridge, one of the world’s leading genome research organisations. Genomics allows us to understand the DNA that is in every species, he says, and this should help us to tackle the current biodiversity crisis.

“One of the goals of the project is that we will really start to understand the processes that generate biodiversity – the processes of evolution. It might let us predict what is going to happen in the future. We really hope to provide an amazing foundation for people to conserve, promote and expand biodiversity. Genetic monitoring is really important in conservation.”

Those on the project also believe that they will provide the raw materials necessary to generate a new sort of economy, he adds. “There are many natural materials out there that are untapped.

“Our hope is that by finding the genetic materials for all these species, we will enable new pharmaceuticals to be found to treat old diseases and new ones. We will make it possible to transition from the carbon-based economies we have at the moment to ones based on natural products.”

Professor Blaxter and his colleagues on the project also believe that it will capture the public imagination. “If every species has its genome sequenced, we are going to change the way people do biology forever.

“It will be an amazing transformation to how we understand the natural world. If you think about it, the human genome was completed about 20 years ago, and that has changed the way we look at human medicine and how we understand human society.

“It will be the same for these genomes. If we have that sort of information for every species, it is going to be transformative.”