Conservation in the Genomic Era

HAVE DNA TECHNOLOGIES REPLACED THE NEED FOR MUSEUMS?


By Sotiria Boutsi, Intern

I am PhD student at Harper Adams University with MSc in Conservation Biology, currently doing a professional internship at the Museum of Natural History in the Public Engagement office. My PhD uses genomic data to study speciation in figs and fig wasps.


The year 1995 marked the first whole-genome sequencing for a free-living organism, the infectious bacterium Haemophilus influenza. Almost three decades later, biotechnological advances have made whole-genome sequencing possible for thousands of species across the tree of life, from ferns and roses, to insects, and – of course – humans. Ambitious projects, like the Earth BioGenome Project, aim to sequence the genomes of even more species, eventually building the complete genomic library of life. But do these advancements help us with conservation efforts? Or are the benefits of biotechnology limited to industrial and biomedical settings?

The value of genetic information is becoming increasingly apparent: from paternity tests and DNA traces in forensic investigations, to the characterization of genes related to common diseases, like cancer, we are becoming familiar with the idea that DNA can reveal more than meets the eye. This is especially the case for environmental DNA, or eDNA — DNA molecules found outside living organisms. Such DNA is often left behind in organic traces like tissue fragments and secretions. Practically, this means that water or air can host DNA from organisms that might be really hard to observe in nature for a variety of reasons — like being too small, too rare, or just too shy.

So, how do we determine which species left behind a sample of eDNA? The method of identifying a species based on its genomic sequence is called barcoding. A barcode is a short genomic sequence unique to a species of organism. Therefore, every time we encounter a barcode sequence, whether it is taken from a living animal or eDNA, we can associate it to the species which it belongs to.

When we have a mix of different species to identify, things become a bit more complicated. Sometimes we will pick up samples which represent an entire ecological community, and must sort through these using a process called meta-barcoding.

How does meta-barcoding work? Well, we want to be able to identify species based on the shortest possible species-specific sequence. Traditional laboratory methods for DNA amplification (PCR) are combined with DNA sequencing to read the DNA sequences found in any given water or air sample. Then, having a database of reference genomes for different species can serve as the identification key to link the sample sequences to the species they originated from.

Pinned insects can be found in the Upper Gallery of the Museum. There are currently 5 million insect specimens at the Museum, serving as a record of biodiversity at the time and space of collection. Museum collections are invaluable ways of monitoring biodiversity but rely on capturing live animals.

So, what does this mean for the future of ecology and conservation? Traditional monitoring of biodiversity can involve capturing and killing live animals. This is the case with insect specimens found in museums across the world. Although museum collections are irreplaceable as a record of the history of wild populations, regular monitoring of endangered species should rely on non-invasive methods, such as meta-barcoding of eDNA. Indeed, eDNA has been used to monitor biodiversity in aquatic systems for almost a decade. Monitoring terrestrial ecosystems through air samples is now also becoming possible, opening new possibilities for the future of conservation.

During March, the Museum delivered practical molecular workshops in our laboratory, reaching more than 200 Key Stage 5 students. Students have had the opportunity to learn about the use of eDNA in ecology, as well as get some hands-on experience in other molecular techniques. These include DNA extraction, PCR, the use of restriction enzymes, and gel electrophoresis.  The workshops were delivered by early-career researchers with practical experience in working in the laboratory, as well as Museum staff with a lot of experience in delivering teaching. Through the Museum’s workshops, which run regularly, the next generation of scientists is introduced not only to both human genetics, but also molecular tools used in ecological research, which without a doubt will become increasingly relevant for future conservationists.

Since 2009, the Museum runs practical workshops for Key Stage 5 students in the molecular laboratory at the Museum’s main facilities. Workshops started again this March, after the mandatory 2-year covid-19 break. Students can learn about and discuss the use of molecular techniques in biology by extracting their own DNA.  

We cannot conserve what we do not know. Monitoring biodiversity is the cornerstone of any conservation practice. Doing it efficiently, by making use of both traditional as well as molecular tools, can allow more accurate predictions for the future of biodiversity under the lens of anthropogenic change.


More Information:

The Roundup on The Great Debate – Do We Need a New Agricultural Revolution?

Post by Dr Caroline Wood


How can we meet the challenge of feeding 10 billion people by 2050 whilst simultaneously addressing climate change, impoverished soils, mass extinctions and unsustainable pollution?

On 20th October, Oxford University Museum of Natural History hosted The Great Debate – an anniversary celebration of the Museum’s Great Debate in 1860, on Darwin’s Theory of Evolution. During this special event, the panel and audience (both in-person and live-streamed) discussed issues, opportunities and tensions relating to the future of food production. By the end of the evening, it was clear that we won’t be able to rely on ‘quick fixes’. Instead, we will need a whole-scale revolution at multiple levels: in our fields, on our plates, and in our attitudes. 


Panel Speakers

Lord John Krebs (Chair) – Former chairman of the Natural Environment Research Committee and Adaptation to Climate Change Committee

Helen Browning – Chief Executive of the Soil Association

Professor Sir Charles Godfray – Director of the Oxford Martin School

Stuart Roberts – Deputy President of the National Farmers Union (NFU)


In our fields

With global food demand estimated to increase by 35% to 56% between 2010 and 2050, it is unquestionable that we will need to keep producing more food. Although the prospect seems daunting, Helen Browning outlined the potential of new technologies to boost yields, including hydroponics and vertical farming; robots that can perform crop care and harvesting; and genetic technologies such as gene editing. However, she warned that the UK is currently ‘way off the pace’, and would remain so until there is more investment in farmer-led research, innovation and knowledge-sharing opportunities. 

As Stuart Roberts pointed out, there are also significant opportunities to boost production simply by addressing inefficiencies and yield gaps. For instance, according to the NFU, if all the 270 million+ dairy animals worldwide were as efficient as UK dairy cows, we would only need 76 million to produce the same amount of milk. New market models, such as direct-to-consumer and digital technologies (e.g. blockchain), could also help reduce the 15% of food that the WWF estimate is wasted even before it leaves the farm

But will increased production come at the expense of damaging natural ecosystems? The new UK Agricultural Act aims to avoid this by providing farmers with a financial incentive to preserve ‘public goods’ including air quality, biodiversity, soil health, and flood mitigation. Sir Charles foresaw that the Agricultural Act will result in a ‘patchwork’ of different farming systems across the UK, each tailored to their locality, with some being highly productive and others more dedicated to public services. 

Debate Panel (Left to Right) – Lord John Krebs, Helen Browning, Stuart Roberts, Prof Sir Charles Godfrey

On our plates

Extensive research indicates that achieving net-zero carbon emissions will require a global reduction in meat consumption and a shift towards plant-based diets. But as Stuart noted, presenting consumers with only the extremes of a carnivorous diet and a vegan lifestyle is not helping this transition. Instead of focusing on binary choices, we should be more concerned with improving the meat we do eat. As consumers, we need to stop seeing food as a cheap, mass-produced commodity, and be prepared to pay a price that will compensate for the development of production systems that are more in harmony with nature. Helen agreed that only by paying more for food can we allow farmers to escape the stranglehold of contracts that pressure them to produce as much as possible, regardless of the environmental cost. However, as Stuart pointed out, to avoid higher prices leading to food poverty, it will be necessary to tackle income poverty first. To this end, he cited Food Foundation research which reveals that the poorest 10% of households would have to spend 76% of their disposable income to meet current diet recommendations.

In our minds

Farmers are critical actors in the global response to climate change, but all too often they are portrayed as villains. Stereotypes regularly cast farmers as chemical lovers who rip up hedgerows and mistreat animals. Instead, we need to recognise and celebrate the farmers who are trying to be part of the solution, including those embracing regenerative farming methods such as pasture cropping, agroforestry, no-till farming and undersowing. Overall, if we want more farmers to become innovators, we need to support them – and as consumers, we can make that choice every time we shop.


The Huxley Room at the Oxford Natural History Museum where the original Great Debate took place in 1860.

Dr Caroline Wood works as a Communications Officer for Oxford Population Health, a department at Oxford University that specialises in global health studies. She is also a freelance science writer, focusing on sustainability, food science and packaging issues. When she is not writing, she enjoys visiting museums (including OUMNH obviously!), hillwalking and painting (badly). 

Crunchy on the outside

By Susie Glover, HOPE Learning Officer

We have an ambitious project underway at the Museum, to preserve a unique and scientifically important collection of over one million British insects. It’s called HOPE for the Future, after the Hope Entomological Collections, and we are keen to shout about how these specimens can help us understand biodiversity, habitats and ecologies.

The learning team behind the project are today launching a new blog for young people interested in entomology. Intriguingly, it’s called Crunchy on the Outside, but please don’t confuse this with the similar, but fundamentally different, mid-’90s advertising campaign for the Dime bar.

A high magnification image of an insect, face-on, showing large proboscis and brown body.
One of many weird and wonderful specimens from our collection, the Acorn Weevil (Curculio glandium).
Here is a peek at some of the tools of the trade, used to move and mend specimens like this moth.

Crunchy will be crammed full of interesting insect info, fun things to make and do, a peek behind the scenes at the Museum, and news from people, past and present, who work in the field of entomology. The odd bad joke may also worm its way in (What do butterflies sleep on? Cater-pillows).

The blog will also be a platform for young people to have their say, about the topics covered on Crunchy itself, as well as on the activity of the Museum. It will give them first dibs on access to related events too. You can check it out, follow, and share at crunchyontheoutside.com.

HOPE for the Future is funded by the National Lottery Heritage Fund.

Swifts flying around the Museum tower

Flight and fight

By Chris Jarvis, Education Officer

Last week’s observations of the swift nest boxes in the Museum tower highlighted the drama the colony faces in the struggle for survival. This week’s survey made that struggle even more explicit…

Clambering through the darkened spaces of the Museum tower, lit faintly by the red lights that the swifts cannot see but which help give surveyors a dim view of the ladder rungs and observation platforms, I peered briefly into each nest box to count the birds and eggs.

In one box I came across a dead bird, alone and lying on its back. Carefully bagging up the body for later investigation I continued my count while pondering the cause of its death, the sadness relieved slightly with the discovery of new eggs in other boxes and the promise of new life to come.

The body of a dead swift found during the weekly survey of the colony of birds in the Museum tower

Screams and banging from birds prospecting for nest sites are a regular backdrop to each survey. Birds call and swoop past the boxes only inches from my ears, separated by just a few roof slates. The birds within scream back in answer. But on this occasion, half way down the tower, I became aware of particularly loud and persistent screams and banging, coming from within a box.

A quick peek inside revealed a hectic struggle between at least three swifts, wings drawn back, wrestling and rolling around, pecking and slashing at each other with their sharp claws. It was actually impossible to see if the fight involved three or four birds as the struggle filled every inch of the small box with wings, beaks, claws and feathers.

David Lack first documented these fights in his excellent book Swifts in a Tower. He proposed that they were the result of birds entering an already occupied box in the struggle to find a suitable nest site.

Swifts flying around the Museum tower
Swifts circle the tower prospecting for potential nest sites, screaming and banging to check which are occupied and which are vacant. Image: Gordon Bowdery

Sitting and anxiously listening beside the box, I recorded the fight lasting 15 minutes from the time I became aware of it. Lack documented ‘gladiatorial shows’ that lasted five and three quarter hours; they were painful to watch, he admitted, as the swifts have a surprisingly strong grip and claws capable of drawing blood, but rarely resulted in death.

When the noise died down, I gently lifted the cloth blind to take another look. Only two birds remained, both looking exhausted and fiercely gripping each other’s feet, one lying under the other. A quick flurry and the upper bird disengaged and jumped from the nest box entrance.

Cover of 2018 edition of Swifts in a Tower by David Lack
Cover of the 2018 edition of Swifts in a Tower by David Lack

Lack also mentions in his book that it is usually the bird underneath in these struggles that is the winner and I was relieved when the remaining bird picked itself up and returned to the two eggs, which had somehow remained in the nest, settled on top of them and preened itself. This suggested that the nest’s original occupant had won, driving off an intruder.

The screaming and banging outside the boxes is a check for a screamed response from within. It reveals whether a box is already occupied or empty, before the bird risks entry. Presumably, the fight I witnessed was the result of a bird not hearing a response or perceiving it as coming from another box.

The drama of the fight illustrates the incredible importance of nest sites and the fidelity the swifts have to them after a year on the wing. Nest sites are at a premium and swifts are almost totally dependent on nesting in old buildings as there are so few forests with suitably old, cavity filled trees remaining.

Once a nest is occupied the owners will fight furiously to defend it and David Lack did record occasional incidents of birds fighting to the death. So perhaps this was the cause of the dead bird I had found lying on its back, but that will have to wait for a later examination.

Meanwhile keep an eye on our nest box; you never know what drama may play out next…

It is important to record nest sites and, if you can, put up nest boxes. RSPB’s Oxford Swift City project, which the Museum and Oxford City Council were involved in, annually surveys and records nesting sites so that development in these areas is restricted during the breeding season and developers must include plans to protect and provide new nest sites when repairs to property or new building takes place. If you would like to help with the work of conserving one of the most dramatic annual migrants to our shores visit the RSPB site.

Through the looking glass

With our Life, As We Know It redisplay project now underway, our Senior Archives and Library Assistant Danielle Czerkaszyn takes a behind-the-scenes look at how we captured the contents of the current displays for the Museum’s archive.

The archive here holds a unique collection of natural history books, journals and documents covering a wide range of subjects related to the Museum’s collections and research. It also contains papers and objects on the history of the building, providing an institutional memory of Oxford’s ‘University Museum’ since its foundation in 1860.

From an archive perspective it was really important to document the current layout of the cases, their specimens and text before they were removed from the court to make way for the new showcases in the first phase of our redisplay work.

The museum in late 2019

The displays as we know them – with exhibitions on the Oxfordshire dinosaurs, Alice in Wonderland, the Oxford Dodo, and more – were last changed in 2000. For the last 20 years visitors to the Museum would remember their first time being wowed by the Megalosaurus jaw – the world’s first scientifically-described dinosaur – or charmed by the Dodo made famous in Lewis Carroll’s Alice Adventures in Wonderland.

Although after 20 years it is time for a change, the stories and information in the displays are too good to be forgotten. So before anything was removed we began to build the archive for the future.

A display of the fossilised remains of Megalosaurus
The previous display on Megalosaurus: The First Dinosaur

The best way to capture all the information of the displays was through high resolution photography, but this was not as straightforward as we hoped.

The first two obstacles to good photographs are pretty obvious to anyone looking at the cases: glass causes huge amounts of glare; and each case has a big dividing line down the centre where the two sliding glass doors meet, cutting what should be a lovely seamless image into two halves.

To avoid glare and the solve the problem of the dividing line, our photographer Scott opened each individual side of the case, photographed two or three images of the display, and then stitched the separate photos together using Photoshop.

Each case was photographed in two or three segments

The segments were then stitched back together and adjusted for exposure and colour balance to create the final image

Another obstacle to taking good photographs of the displays came from the Museum itself. Some of our larger display furniture, such as the glass case for the Atlantic Bluefin Tuna or the huge T. rex plinth – got in the way of a nice straight shot. Because these items are so large and heavy they were impossible to move, so we had to improvise and do our best.

Capturing the displays before the current cases were removed allowed us to keep an archival record of their contents

Thankfully, we managed to get shots of all 24 displays before they were removed and so a record of each case now rests with the Museum’s archive. If anyone wants to know what the display cases in the court looked like from 2000 to 2020, they will now be able to look back at the images in the archive and recall the magic of the Oxford Dodo exhibit that perhaps first made them fall in love with the Museum.

Our new displays are now in development, and will include some beautiful presentations of the diversity of life, looking at the importance and fragility of biodiversity and human impact on the environment. These new exhibits will show how the biological processes of evolution combine with the geological processes of our dynamic Earth to give rise to the immense, interconnected variety of the natural world.

We look forward to telling you more about that here as the project progresses.

The Life, As We Know It redisplay project is supported by a generous grant from FCC Communities Foundation.

Mammoth tusks and cocktail sticks

By Pete Brown, Move Project Assistant

As part of the Museum of Natural History Move Project Team I have helped move and repackage tens of thousands of specimens since 2017, removing boxes filled at any time over the last 150 years from their old storage location in a deconsecrated church building near Oxford.

At our new facility we have been documenting and repacking the contents in new, clean containers and placing them in environmentally stable, safe warehouses specially adapted for museum storage.

Some objects are trickier to store than others. Things that are long, heavy, curvy and fragile are tricky. Mammoth tusks are long, heavy, curvy, and fragile. This means:

  1. They’re not going to fit in a normal box.
  2. They’re going to be difficult to move around.
  3. That beautiful curve will mean that all the weight of the tusk may be bearing down on just two small contact points where the tusk meets the storage surface.
  4. Because those points are fragile, they’re likely to get damaged.

A lot of weight can rest on small areas of the tusk, putting strain on the specimen and potentially causing damage

The tusk in this article is a prime example. The area nearest the camera in the photo above provided just a tiny point of contact with the floor and was very loose, almost to the point of detaching. It needed to be repaired, and stored in such a way that it wouldn’t get damaged again.

Pete Brown carries out delicate conservation work on the mammoth tusk

I filled some of the missing areas around the fragile area with an easily removable fine acrylic putty to prevent further movement and loss of the original material. A cotton tape sling helped to suspend the fragment in place during the work.

Thick plastazote provided a sturdy, slightly yielding bed for the tusk to lie on in storage, but to prevent the tusk from getting damaged again more needed be done to reduce the pressure on the points of contact.

The dark grey foam material, plastazote, is often used as a cushioned support for museum objects

I cut depressions into the plastazote where the tusk naturally lay to increase the total surface area supporting the weight of the tusk, and fixed plastazote wedges and supports in place with cocktail sticks to again increase the contact area and prevent movement. Cotton fabric ties, fed through slits in the plastazote, also helped to guard against unwanted movement.

Cocktail sticks: not just for cheese and pineapple

The repaired end of the tusk is now only supporting a fraction of the weight it used to, and once the tusk and the plastazote bed are placed into their new custom-made crate it will be ready for long-term, safe, damage-free storage!

The end of the tusk after treatment

To keep up with all the move project action, follow the museum hashtag #storiesfromthestore on Twitter @morethanadodo.