At the Natural History Museum, London, we provide global open access by default and share our digital collections data on the Museum’s Data Portal.Continue reading “Addressing planetary challenges with open data”
We are currently digitising 75,000 freshwater insects belonging to three small orders. The presence of these groups can give us an idea about the water quality of the river they live in. As August is #WaterQualityMonth we thought this would be a great time shed some light on these orders of insects that you might not have heard much about before.
A guest blog by Galina Jönsson
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?
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.
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.
Solving the statistical riddle
As a masters student, I naturally felt drawn to solving the statistical riddle and embarked on modelling social wasp trends using the Museum’s collection alongside survey data from the Bees Wasps and Ants Recording Society. Our study extended existing trends by 70 years, and indicated that agricultural intensification drove a 70% decline in English hornets (Vespa crabro) between 1950 and 1970. This was followed by a northward range expansion facilitated by climate change-induced warming. Today, hornets have bounced back to 1950-levels in terms of numbers but are more sparsely distributed over a larger area. Through this study, we demonstrated that specimen data from collections can produce long-term population trends, but thoroughly addressing questions of human influence requires more museum data, both species and specimens per species.
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?
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.
A collaboration between Adobe and the Natural History Museum, London
Award winning digitisation
The Natural History Museum Digital Collections Programme has just received a lovely Christmas present! Following our November win as best Not for Profit project of the year in the UK IT Industry Awards, we’ve just been notified that we are also winners in the Culture and Tourism Category of the World Summit Awards. Continue reading “Over half a decade of digitisation | Digital Collections Programme”
Digitisation enables us to understand exactly what we have in the collection. This can provide updated and accurate collection records, improve estimates for digitising future collections and occasionally uncover the unexpected. Continue reading “Digitisation uncovers rare specimens that highlight the diversity of sex in nature| Digital Collections Programme”
A guest blog by Lizzy Devenish
In preparation of this blog I’ve been asking myself what, exactly, do I do for my job. “Well,” I say, “I’m a digitiser – I assist in the digitisation of specimens.” “Fantastic!” you say, “but what the hell do you do?” Continue reading “Day in the life of a digitiser |Digital Collections Programme”
A Guest blog by Robyn Crowther and Blanca Huertas
Some of the Museum’s invaluable butterfly reference material, previously only accessible to a handful of scientists, has been released onto the Museum’s Data Portal. Over 90% of these specimens were designated as types in the 21st Century, but this is the first time that images of many of these species have been freely accessible to the global community.
My type on paper
When scientists describe and name a new species, they aren’t actually describing every individual that belongs to that species. Instead they select one or a few specimens with ‘typical’ characteristics representing a species to write a detailed description. These name-bearing specimens are known as types, and are used as a reference when identifying and grouping other individuals into that species.
A type bears not only a name, but a big responsibility. If you want to identify and name specimens you have observed or collected you need to look to the type (or an illustration of it) and compare the key characteristics that make that species unique and different from others. For this reason, types are arguably some of the most important specimens in a collection and a priority for digitisation projects.
Recently, the Museum’s butterfly types have been separated from the main collection into a new seperate collection, making it easier to find, use and reference them. To make these types even more accessible, it was also decided that this collection would be digitised and made available on data.nhm.ac.uk – separate curation first makes digitisation of these collections much more efficient, removing the need to ‘pick and choose’ from many different collections drawers.
We digitised 1000 specimens, covering 220 species. These specimens were collected from 46 countries, representing all continents. The oldest type in this project was designated in 1939 and the newest in 2017.
What’s in a name?
Digitisation isn’t just about capturing an image of a specimen. Before these butterflies were ready for their close ups, extensive curatorial work was needed to prepare the collection, ensuring that each specimen is associated with the correct taxonomic information (e.g. the species and genus names are correct).
Among these specimens, we found various examples that illustrated the importance of this digitisation project. For example, six specimens used to describe the species Cacyreus niebuhri, an African species, in 1982, had no identification labels or registration information when they were found in the mixed collections – they had lost their name!
As part of this project, an investigation was mounted to discover the true identity of these six butterfly types. Fortunately, information about when and where the specimens were collected was available on the labels pinned underneath each butterfly, with a small label from the author stating they were part of a type series.
The specimen labels indicated that they were collected in the Republic of Yemen by “T.B. Larsen” in 1980. A former Scientific Associate of the Museum, Dr Torben Larsen was a world renowned expert on butterflies of Africa and wrote many books on the subject. A search of his name, along with the collection event details from the specimen labels, threw up the only book on butterflies written from the area and at the time of the species’ description in 1982. Although the book is currently out of print, “The Butterflies of the Yemen Arab Republic” is available at the Museum library and had been digitised so we were able to search the text. As we knew the family that these butterflies belong to, we were able to find the description and images of the mysterious specimens and their name. Cacyreus niebuhri – named for the 18th century Danish topographer Carsten Niebuhr, one of five men who took part in an ill-fated expedition to Yemen that saw him as the sole survivor.
Further searching online revealed that Larsen’s book is the only place that any images of this species can be found, including recent revisions and websites describing the species. The images included in the book are of a quality that makes it hard to identify important diagnostic characteristics, and resolution is even lower in the digitised copy of the book. Type specimens are the reference material for any specimen identification, so without access to a detailed image, identifying anything as C. niebuhri becomes extremely difficult, leading to misidentifications or no identifications at all. The quality of the images that we have released on data.nhm.ac.uk help to address this problem.
Above left: The Museum’s image of the paratype specimen of Cacyreus niebuhri. Right: The only reference image available for C. niebuhri before this project.
Sharing is caring
By sharing data about our specimens we provide a resource that can be used by the scientific community and the public in a number of ways. One of the reasons museum collections remain such an important scientific resource is because they provide a window into a species’ past, allowing us to compare them over time and space, revealing if and how their distributions have altered with the rapidly changing environment. This all starts with being able to give members of the same species the correct name, so that the comparisons are meaningful.
C. niebuhri, a member of the Lycaenidae family, is endemic to the Republic of Yemen, only occurring on the upper reaches of the wetter mountains of that country. These mountains form part of the Arabian Peninsula ecoregion, a region that supports thousands of unique plants and animals and one that is increasingly under pressure from deforestation and soil erosion. Any work aiming to mitigate these pressures on endemic species needs first to know what species occur in this area so that their populations can be monitored. Comparing individuals currently in the area to a name- bearing type specimen should make this easier.
Dingana alaedeus is another example of an endemic species that the Museum holds type material for. Commonly known as the Wakkerstroom widow, this butterfly is found only in South Africa’s high altitude grasslands at elevations of about 2,000 meters and classified as “Near Threatened” during the 2013 Conservation Assessment of Butterflies for South Africa. Similar to the previous example there is little information relating to this species online, with the same single image being used on several different online resources. In fact, for most of the 220 species we have digitised during this project the images that we have uploaded to the Museum’s Data Portal are the first and only images to be easily accessible online.
Unlocking the Museum’s collections and making them available to all is the mission behind many of our digitisation projects and is one of the Museum’s strategic priorities. There are over 1.5 billion natural history specimens in collections around the world. They have the potential to play a critical role in addressing the most important challenge that humans face over the next years: how to map a sustainable future for ourselves and our changing planet. To see the butterfly types digitised during this project, and over 4.3 million other specimens, visit the Museum’s Data Portal.
Over the past year the digital collections team have worked on incredibly varied projects across multiple collections in the Museum. Continue reading “Digitising the Collection in 2018”
Guest Blog by Phaedra Kokkini
This is the second part of the story behind about the ALICE pilot project. While the first part focused on piloting our ‘Angled Label Image Capture and Extraction’ or ALICE, this part will focus on the collection and collector. Quite unexpectedly, while preparing our chosen collection for imaging I got to know a person through his collection of pinned insects. Continue reading ““Mr. Cooper, meet ALICE.” – Part 2 | Digital Collections Programme”