The UK holds hundreds of millions of natural history specimens of scientific importance. Exactly how many specimens and what those specimens are, is currently unknown. Unveiling the contents of the UK’s collections will open the door to further digitisation and unlock the full scientific potential of UK natural science collections.
Digitising, the process of converting physical information into a digital form, the UK’s natural science collection, opens up a unique and valuable national resource to the world and enable the UK to be part of current and future scientific collaborations to find solutions to the biggest challenges of our time.
Nearly two years after the first case of COVID 19 we are still dealing with massive human health impacts and changes in our daily lives, but how can digitising bats help prevent future pandemics?
Left: The woolly monkey (Lagothrix lagothicha) photographed by Evgenia Kononova via Wikipedia Right: The Scientific paper that inspired this blog.
In this blog, we’re looking at a recent paper that cited some of our data in investigating the conservation potential of protected areas of rainforest using data on the Woolly monkey (Lagothrix lagothricha).
From Left: Galina Jönsson in the Museum collection, The Museum’s Data Portal and graph showing scietific paper rates and numbers since 2015.
Digital Collections support over 1000 scientific papers
The Museum’s Data Portal was launched in December 2014 to provide access to Museum collections and research, enabling to explore, download and re-use these data for their own purposes. Museum collections include specimens collected over the last 200 years, a critical time period, during which humans have had a major impact on the distribution of biodiversity.
Since 2015, more than 1000 research papers have cited data from the Data portal and partner platforms like the Global Biodiversity Information Facility (GBIF), covering topics including agriculture, biodiversity, evolution, ecology, species distributions and human health. This blog looks at just one of the studies using Museum data, PhD candidate Galina Jönsson’s research using data to examine how human activity has impacted butterfly populations over the 20th Century.
Insects are declining at alarming rates, but we do not precisely know why. From wasps to butterflies, Galina is looking for answers in the Museum’s pinned insect collection and extending time series to span the period of accelerating human pressures like agricultural intensification and deforestation. ‘At first glance, my results suggested that British insects fared pretty well, but I quickly realised there is much more to this than meets the eye.’
Blame eccentric Victorians or lazy statisticians?
A graph showing rates of butterfly distribution change over the last century
Natural history collections’ pinned insect specimens have revealed fascinating changes over the last centuries but have rarely been used to map how, and why, some species increase while other decrease. Nearly everything we know about insect responses to human activities comes from survey data collected by national schemes like the UK Butterfly Monitoring Scheme (UKBMS), which was launched in 1976. One of the benefits of using survey data is that it is standardised, meaning that all species at a particular location are recorded in the same way, at the same time of the year, for multiple years in a row. This makes it easy to compare how different species change in population or geographical location over the years. In the UK, which is unusually well-documented, our knowledge from such survey data is limited to the period since 1970. This period falls after most large-scale transformations of the British landscape such as the agricultural intensification of the 1950s with its deforestation and increased pesticide-use. As a result, we find ourselves without baselines reflecting the state of biodiversity prior to major human pressures.
In contrast to survey data, museum specimens do go back much further in time to give us these baselines – but they were not systematically sampled. This challenges conventional statistics. Labels inform us where and when specimens were collected, but not how. Just like millennial houseplant enthusiasts, Victorian bug collectors had individual preferences. Some travelled far to collect one specimen of every species, others collected every tiny variation within their favourite species. Some collectors were working scientists, but a lot of the collection comes from amateurs and those that collected as a hobby, so the type of specimens and data that was recorded also varies due to the collector.
Amateur collectors can match or exceed the standards of scientists who were paid for their work. Robert ‘Porker’ Watson (1916-84) was a tax accountant and ‘amateur’ butterfly collector and breeder whose setting of specimens was described as ‘a miracle of perfection’ Aurelian Legacy, British Butterflies and their collectors (Salmon.M.A et al, 2000 p230)
Ambitious digitisation projects are making collections available with the click of a button; and in addition, now, citizen science projects generate enormous amounts of contemporary data in addition to data from collections and systematic surveys. Smartphone applications let anyone submit wildlife sightings in seconds but, just as collections reflect eclectic Victorians, citizen scientists’ preferences introduce their own set of biases to the data. We need new statistical models to extract the valuable yet varied information museum specimens, survey data and citizen science sightings hold, but the models also need to handle their respective biases.
The European hornet (Vespa crabro) and its distribution in the UK over the last 120 years.
And in flew century-old butterfly specimens, forming the basis of my PhD research. In the interest of honesty, perhaps I should say ‘in flew iCollections’, NHM’s pilot mass digitisation project that digitised over half a million British butterflies and moths. My current research explores temporal patterns of British butterfly trends across centuries, looking at how the timings of major changes to butterflies coincide with habitat changes, and how species-specific characteristics affect population-level change. There are 59 British butterfly species; another five species have become extinct in the last 150 years. Butterflies are sensitive to temperature and weather conditions, and caterpillars are picky eaters, some accept nothing but one specific host plant. These factors render them particularly vulnerable to, and simultaneously good indicators of, greater habitat and climate changes.
Generalisations hide uncomfortable truths
After a couple of years formulating the perfect model (hint: there is no such thing as a ‘perfect model’), I summarised the trends across all British butterfly species. The preliminary results were surprising. Averaging across species, there has been a 15% decrease since 1900. But we know that humans have extensively altered 75% of Earth’s surface, so this had me wondering – is a 15% decrease over 120 years really that bad?
Distribution change of all species of british butterflies
Distribution change with generalists and specialists split out
Next, I grouped species according to whether they are specialists requiring specific habitats (the picky eaters) or generalist wider countryside species that can use a range of habitats. The generalist species nearly doubled since 1900, whilst the specialists had halved. Separating specialists from generalists also showed that the most dramatic changes occurred before the 1970s baseline that many recording schemes give us. Just like the hornets, specialist butterflies started to plummet around 1950, but in contrast to hornets, they did not recover after 1970. It appears that agricultural intensification in the 1950s triggered the troubling subsequent declines (or at least was the straw that broke the specialist’s thorax). Wider countryside species also began expanding in the 1950s, and this expansion continued into the 2000s.
What is wrong with generalists?
Overall, preliminary results show that we’ve lost around 15% of British butterflies since 1900. Specialised species have plummeted, but generalist wider countryside species are making up for the losses. Sometimes people ask ‘what is wrong with generalists?’ – does it really matter which butterfly species are in the ascendant? It all comes down to biodiversity. The diversity of life on Earth, which we need for human well-being, prosperity and ultimately, survival.
Species richness is the number of different species in an area, a way of measuring biodiversity. When the number of species thriving in an area declines or becomes unbalanced, certain species that are doing well can come to increasingly dominate the area. The species that can’t adapt are put under further pressure from the increasing generalist species eating their food or nesting in their areas. A change to the delicate balance of the species in an area can reduce biodiversity and species richness, cause extinctions and dramatically change ecosystems.
The wall butterfly (Lasiommata megera) distribution change over 20th century
However, is it fair to divide all butterflies into either habitat generalist or specialists? And assume that, within each group, every species shows the same long-term trends? Although a habitat-use separation can give useful indications, the reality is much more complex. For instance, the wall butterfly (Lasiommata megera) has suffered worrying declines despite enjoying a variety of habitats. With rising temperatures, the cold-loving wall butterfly has been forced northwards and risks joining the list of butterflies that are extinct in Britain, when it reaches John O’Groats. Biologists often divide species by habitat-use, but the dramatic decline of the wall butterfly shows us that every species has its own particular quirks, extending beyond habitat-use. In addition to temperature-tolerance, species differ in a number of characteristics like their reproduction strategies (for example, many tiny eggs but few survive or a few huge eggs with high survival), the ease with which they find a mate, and how strong flyers they are (which determines if they can colonise new habitats). I am currently using several such species-specific characteristics to identify combinations of characteristics that predispose species to being particularly vulnerable and give others the ability to rapidly expand.
Natural history collections’ specimens are vital to gather the data needed to extend time series of species’ trends to periods prior to extensive anthropogenic pressures and provide important novel insights into our effects on biodiversity. However, most specimens world-wide are relatively inaccessible to research, hidden away in undigitised collections. Mobilising digitisation projects that provide open access to this important biodiversity data will allow us to refine models, produce more accurate future projections, and make effective conservation decisions to bend the curve of global biodiversity loss.
We would love to hear from you if you are using data from data.nhm.ac.uk please get in touch or stay up to date with Digital Collections news by following us on Twitter and Instagram. Keep up to date with our blog posts for more examples of our data in action.
If you are spotting butterflies this summer please log your findings on a recording scheme so that researchers like Galina can make use of your work. You can also follow Galina on Twitter to keep up with her research.
Adults of these species are attracted to the light of a moth trap of course! In this instance I am not referring to the Common Swift bird (Apus apus) that is seen carrying out impressive aerial displays in summer but instead to the beautiful Common Swift moth (Korscheltellus lupulina).
It’s been a year since we had to first close the doors of the Museum due to the pandemic, and like the rest of our colleagues, the Digital Collections Programme (DCP) team have adjusted to the world of video calls, furlough and working from home. Despite these challenges, in 2020 the team imaged 72,000 specimens, transcribed data from 85,000 specimens and georeferenced 17,000 specimens, giving us plenty of progress to reflect on from this challenging year. Over 25 billion data records have now been downloaded from the Data Portal and GBIF in over 360,000 download events, and remote working has only further highlighted the pertinence of digitising collections and making them accessible to the world.
Ephemeroptera (mayflies), Plecoptera (stoneflies) and Trichoptera (caddisflies) – or EPT for short – are three orders of insects found in freshwater systems across the world. These three key groups are important bioindicators, meaning that their presence and the size of their populations can give us an idea about the health of a freshwater habitat. There are approximately 89,000 specimens in the Museum’s EPT collection, and the Digital Collections Programme (DCP) are in the process of digitising them. Mobilising this data will aid research being undertaken by the International Union for Conservation of Nature (IUCN), to further our understanding of EPT distribution and assess these species’ vulnerability to extinction.
While Charles Darwin was travelling on the Voyage of the Beagle, he found thousands of shells and hard parts of marine animals on land, far away from the sea. This shaped his and our current understanding on how the South American continent has changed overtime. In this blog, Lucia Petrera takes us behind the scenes to explore how these fossils will be protected and shared with the world.
The project to conserve and digitise the fossils collected by Darwin began with the fossil mammals collection. Thanks to the generosity of the Hartnett Conservation Fund we are now able to include the other fossils collected by Darwin which form part of the Museum collections. We are currently working to conserve and digitise around 255 marine fossil invertebrates collected in South America from 1831-1836.
They include:
• Brachiopods, or lampshells, which first appear in the fossil record 550 million years ago and are still alive today • Ammonites, which are coiled shelled molluscs related to octopuses and squids, which first appear in the fossil record 420 million years ago and are extinct • Bivalves, the group of molluscs that includes mussels and clams, which first appear in the fossil record 520 million years ago and are still alive today • Gastropods, the group of molluscs that includes slugs and snails, which first appear in the fossil record 500 million years ago and are still alive today
First ammonite in South America
Image of NHMUK PI C 2612, an ammonite in the genus Maorites one of the first ammonites recorded from South America with the original red rectangular Darwin labels.
Many of the specimens that Darwin collected are ‘type’ specimens – they were a new species, unknown to science at that time. Darwin collected one of the first ammonites ever recorded from South America, from Mount Tarn in Tierra del Fuego, Chile. Ammonites are excellent ‘index fossils’ – fossils that are often able to be used to identify the geological time period they existed in. Darwin enlisted assistance with the identification of the material from experts at the time, including Alcide D’Orbigny, a French naturalist. Initially this specimen was identified as Ancyloceras simplex, a European ammonite. However, more recent re-identification has placed it in the genus Maorites. Maorites is from the Late Cretaceous period (100-66 million years ago) and found only in the southern continents such as South America, Australia, and Antarctica, the continents that were part of the ancient super continent Gondwana. Gondwana gradually broke up 180 – 80 million years ago, carrying its cargo of ‘Gondwanan’ fossils on each of its constituent continents.
A map showing the continents that made up Gondwana. Image: United States Geological Survey via Wikimedia Commons.
Miles of seashells
NHMUK PI G 25287 Adelomelon alta, a carnivorous snail from Santa Cruz in Argentina. This species lived in shallow seas on sandy bottoms where they can find clams to pry apart and eat.
Fossils can be also indicators of past habitats and geological processes, and some of the marine shells collected by Darwin told a fascinating tale. Darwin observed marine shells along 1200 miles (1900 km) of coastline on what he called ‘successive beaches’- geological features now known as ‘marine terraces’. A marine terrace is any relatively flat, horizontal, or gently inclined surface of marine origin, bounded by a steeper ascending slope on one side and by a steeper descending slope on the opposite side. Darwin theorised his ‘successive beaches’ extended to 1600 miles (2600 km) or more. He collected his thoughts in an essay entitled ‘The Elevation of Patagonia’, documenting his model for the formation of successive beaches. This challenged his geological learning from Charles Lyell’s Principles of Geology, that had supposed elevation change to be much more localised. Darwin’s conclusions are confirmed by geologists today, and his successive beaches were most likely formed during ice ages alternating roughly every 100,000 years between glacial and warmer periods. During the glacial periods much of the world’s water was locked away and sea level fell by about 100m. In warmer times, the sea rose and areas were flooded again. This interplay of sea level change and regional uplift is why Darwin found so many marine fossils at high elevations and in some cases far from the sea. Some specimens Darwin found were species that could still be found living on local coasts, which told him that this land change happened relatively recently. One of Darwin’s major achievements on the Beagle voyage was his discovery that much of the southern half of South America had been uplifted in relatively recent geological times.
Preserving Darwin’s Legacy
NHMUK PI G 26369-26370-26371 Three specimens of the Plio-Pleistocene carnivorous gastropod Chorus blainvillei (d’Orbigny) from Coquimbo, Chile. Before and after restorage.
To conserve these specimens, we need to keep them in a stable environment to minimise the risk of damage to them during handling and storage. We use conservation grade inert materials to re-house these specimens so that they will be kept in the same condition for many years to come. Due to the historic nature of this collection, some of this work has involved the fabrication of bespoke supports suited for long-term preservation. For example, some of Darwin’s brachiopods were stored on old wooden boards using nails to keep the specimen in place. At the bottom of each board there is a handwritten label with the specimen’s data. As we want to both conserve the specimen and the historical label, this required some creativity. These nails are ordinary builders’ nails, however due to the metal in the nails being lot harder than the soft rock of the fossil shells, this can cause abrasion and leave grooves where they touch the specimen, so needed to be removed. After removing the nails, the board was partially padded using Plastazote® foam which was cut to the exact size needed to support the specimens. This prevents movement, further abrasion and damage, while leaving the label area uncovered so that the important collection data, such as species name, collections site and date can be read.
NHMUK PI B 18170 Terebratula, a filter feeding invertebrate.
NHMUK PI B 18170 Terebratula, a filter feeding invertebrate.
NHMUK PI B 18170 Terebratula, a filter feeding invertebrate.
NHMUK PI B 18170 Terebratula, a filter feeding invertebrate.
NHMUK PI B 18170 Terebratula, a filter feeding invertebrate.
NHMUK PI B 18170 Terebratula, a filter feeding invertebrate.
In addition to conserving and re-storing the specimens, we are also photographing and capturing associated data on the specimens to be released via the Museum’s Data Portal. High resolution photographs are being taken so that all angles and defining characteristics of the specimen, as can be seen with the image of Terebratula above. Terebratula had a fleshy stem protruding from its shell that it used to attach to something hard and firm such as a rock. To feed, they open their shell and the sea water (containing small food bits) circulates and the animal uses its filter feeding organ to get the nutrients it needs. Researchers use these example specimens as reference material and will want to be able to clearly see the characteristics unique to that species.
All of these specimens had a significant impact on Darwin’s thinking. By fully digitising the specimens, researchers all over the world working in taxonomy, geology, biogeography, ecology and more will be able to access high resolution photographs and specimen data from these historically and geologically important specimens without travelling, continuing the long process of study of those specimens started by Darwin himself. Read more about other parts of Darwin’s collections that we are digitising in our previous blogs or stay up to date the Darwin digitisation project by following @NHM_Digitise and @NHMfossilmammals on twitter.
Access to natural history collections can be added to the ever-growing list of things that became virtual in 2020. Along with virtual coffee breaks, virtual meetings and the ubiquitous virtual pub quizzes, SYNTHESYS+ users are now able to request Virtual Access to natural history collections.
