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?Continue reading “Bats about Data”
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.
Since 2015, the Natural History Museum London has made its research and collections data available through its Data Portal. Some important new features have just been added which make it easier for users to reuse this data. Continue reading “Our Evolving Data Portal | Digital Collections Programme”
On Friday 28 September we took part in European Researchers Night and tried something new with museum visitors. We have been experimenting with recreating photographs that contain digital specimens in place of the usual pixels. Continue reading “Portraits inspired by data |Digital Collections Programme”
In collaboration with the NGO Ecotourism and Conservation Society Malaysia (ECOMY) we have begun a new digitisation project to digitise the Museum’s collections that occur in Malaysia and its surrounding regions.
This project will image representatives for each species across a range of insect groups and will release the digitised specimens openly on the Museum’s Data Portal. In addition, we will be digitally sharing these specimens and their data to our Malaysian colleagues for use through their own online platforms.
The final batch of data from the iCollections project has now been released through the Museum’s Data Portal – a total of 260,000 Lepidoptera specimen records, bringing the total number of Museum specimen records accessible on the Portal to just over 3.8 million.
What was iCollections?
In 2013 the Museum started to look at the best way to digitise Butterflies and Moths from the UK and Ireland, a collection estimated at half a million specimens. This was a pilot project to develop quick and efficient ways to digitise large Museum collections.
During the pilot project we trialled and adapted methods of image capture to suit the specimens, giving us an efficient workflow which can be used to digitise wider pinned insect collections. We place each specimen in a specially designed unit tray, with raised sides where we position the specimen’s labels and add a barcode encoded with the unique specimen number. We place each tray in a light box under a DSLR camera to capture an image containing the majority of specimen data. These images are ingested into a bespoke database, which allows species name and location (within the collection) to be added to the file. The database transcription interface lets us add additional data from labels.
During the iCollections project, we became much more efficient with the time taken to photograph a single specimen, whilst ensuring that the damage to these precious specimens from handling is kept to a minimum. We digitised the entire butterfly collection of over 180,000 specimens and made a significant start on the moths by digitising over 260,000 specimens.
In 2016 we secured further funding to carry on the digitisation of the British and Irish moths with our refined workflow. Once this has been completed, further data will be released on the Data Portal. When complete we will have just over half a million Lepidoptera specimens accessible to anyone in the world with an internet connection. This enhances access to our collection, which traditionally will have been via visits or specimen loans. In some cases the researcher may only require a digital specimen, or the digital records could help a researcher narrow down the scope of what they may want to study on a visit to the museum.
iCollections enabled us to come up with an efficient and bespoke workflow for pinned insects which we have been able to re-use. We have published a paper on the iCollections method, to share this with the natural history community. We have also used the learning from iCollections to start new projects, such as our current project to digitise Madagascan Lepidoptera type specimens.
Why Butterflies and Moths?
The British Lepidoptera collection contains over half a million pinned specimens collected in the UK and Ireland spanning over 200 years. It includes donations from important collectors of the twentieth and twenty-first centuries. As we digitise the Lepidoptera collections we are georeferencing each record, mapping the distribution of species and revealing collecting trends since the mid-nineteenth century.
By providing access to this unrivalled historical, taxonomic and geographical data we can equip more scientists to conduct new research in new ways. For example, Museum scientists, Steve Brooks et al. have been able to compare butterfly data to historical temperature records and found that 92% of the 51 species emerged earlier in years with higher spring temperatures.
‘The warming climate is already causing butterflies to emerge earlier – and unless their food plants adapt at the same rate, the insects could emerge too early to survive.’ (S.Brooks et al., 2016)
When it comes to digitising Lepidoptera, our digitisers can now process up to 300 a day. They get to see and interact with the specimens up close and become extremely fast with a pair of forceps! Our digitiser Peter Wing told us “My favourite image to digitise was a Monarch Butterfly that was pinned with a sewing needle.” While digitising, we uncover some fascinating stories behind the collection. We have been sharing some of these enlightening moments by using #MothMonday on twitter.
Who’s using our data?
We are on a mission to digitise the Museum collection of 80 million specimens. We want to make available our unrivalled historical, geographic and taxonomic specimen data gathered in the last 250 years available to the global scientific community. These data, along with associated specimen images are released through the Museum’s Data Portal.
Through the Data Portal and those of our partners like the Global Biodiversity Information Facility (GBIF), more than 5.9 billion records have been accessed in over 115,500 downloads since April 2015. Through GBIF we are also able to see which scientists are using our data as part of their papers and through Altmetric how many people are talking about our data online. So far we have been cited in 44 papers and referenced over 100 times online.
The Data Portal currently has around 200 non-museum users each day and contains more than 700,000 species-level (index lot) records and over 90 research datasets uploaded by NHM staff and other institutions. This includes 3D scans, images and audio recordings as well as more traditional data.
Critical information is currently locked away within hundreds of millions of specimens, labels and archives in collections across the globe. Our ultimate goal is to unlock this treasure trove of information so that scientists, researchers and data analysts from around the world can use this information to tackle some of the big questions of our time.
To make use of the Museum’s iCollections data please visit the Data Portal To hear more stories behind the Lepidoptera collection you can follow our #MothMonday content on twitter or keep up to date with the Museum’s digitisation projects on the website.
With good weather forecast for most of the UK this coming weekend, and local schools breaking for half-term, many of you will be making a bee-line for the coasts… where you could be rock-pooling for science!
The Big Seaweed Search
Our Big Seaweed Search invites you to take photos of seaweeds and submit your observations online to help Museum researcher Juliet Brodie better understand how rising sea temperatures and other changes are affecting our beautiful seas.
You can request a free Big Seaweed Search guide by emailing your name and postal address to firstname.lastname@example.org, or download and print your own to find out how to take part. In fact, the Museum is celebrating the oceans this year, and there are many ways to get involved in our year-long exploration of the marine world! Continue reading “Take part in ocean science – on the beach or from your computer! | Citizen Science”
Natural history collections provide an enormous evidence base for scientific research on the natural world. We are working to digitise our collection and provide global, open access to this data via our Data Portal.
To digitise the collection we are developing digital capture flows that cater for a wide range of collection types. One of the applications we have developed is Inselect – a cross-platform, open source desktop PC application that automates the cropping of individual images of specimens from whole-drawer scans.
Our previous blog post looked at preparing the Lepidoptera for digitisation. In this post, we will look at the second part of the digitisation process; the imaging and transcription that allows data to be set free and accessed by the global science audience on the Museum’s Data Portal.
Let’s find out what’s involved and why it’s leading to new ways of accessing and using the information in our collections. Continue reading “Our butterfly and moth data takes flight! | Digital Collections Programme”
We have a massive digital challenge. How do we transform museum collections of millions of diverse specimens, each with complex information in many forms, into digital resources – images and data – to be used by modern science and shared across the world?
The collections have been at the centre of scientific knowledge for 300 years – how do we take them into science’s future? In the words of Rod Page from Glasgow University: how do we transform a 19th Century technology into a 21st Century technology? This is the question we have been looking at in a Cisco Pitstop at the London Digital Catapult Centre over two days in February 2016.