The Natural History Museum’s Digital Collections Programme

Crowdsourcing our data in 2017

The Digital Collections Programme at the Natural History Museum in London

The Digital Collections Programme has run two crowdsourcing projects on Notes from Nature in 2017. We wanted to say a massive thank-you to the 2,000+ volunteers who together have helped us to capture data from over 15,000 specimens this year. You have made a significant contribution to Science.

1) collage for blog

Crowdsourcing our data in 2017

We can digitally image individual microscope slides at a rate of up to 1000 slides per day, but we still need help with capturing the label information on each slide. Transcription is an essential part of our digitisation process.

By reading the labels and typing information such as the collection date and location into the relevant data fields, our digital volunteers make it possible for us to release this data freely and openly on the Museum’s Data Portal. This data is available worldwide for researchers to study and explore.

Over the past year we showcased our crowdsourcing projects at the Lyme Regis Fossil Festival, Science Uncovered 2017 and the global WeDigBio transcription event. We have also hosted 14 Visiteering Days, in which over 120 people took part. Anyone interested in taking part in our one-day Visiteering programme to support the Museum’s work can register online here.

The Killer Within: Wasps, but not as you know them

Fairy fly

Fairyflies average at only 0.5 to 1.0 mm long

Our first crowdsourcing project within the Digital Collections Programme consisted of 6,285 microscope slides containing tiny parasitoid wasps called chalcids (pronounced ‘kal-sids’), which lay their eggs inside other insects. Chalcids are the natural enemies of many insect pest species that damage our food crops, and are therefore used commercially as biological control agents.

Thanks to the help of over 1,300 digital volunteers for the Museum, the scientific information contained on these microscope slide labels have now been fully transcribed and are currently being processed for publication on the Data Portal.

From this data we learned that John S. Noyes, formerly of the Natural History Museum and developer of the Universal  Chalcidoidea Database, was our most active collector, that the majority of the specimens were collected in the 1980s and that the UK is the most prominently represented country in this collection.

Recently, we have been digitising the Museum’s parasitic louse slide collection – consisting of 70,667 slides at present. For each specimen, the whole slide has been imaged in to capture both the specimen and the labels.

From this collection we have isolated two subsets of louse specimens for two different crowdsourcing projects, each of which trialled a new platform for the transcription effort: lice from marsupial mammals – ‘Boopidae of Australasia’, hosted on DigiVol, and Lice of the Open Oceans, hosted on the Zooniverse.

 

Miniature Fossils Magnified: The smallest shells in the ocean

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Foraminifera can help us learn how our ocean has changed over 500 million years

Our Miniature Fossils Magnified project features a collection of ~ 3,000 microscopic fossils, called foraminifera (or forams for short), embedded in slices of rock. The Museum has a strong tradition of foraminifera research dating back to the late 1800s, and the foraminifera collection – with approximately 250,000 slides – is one of the the most extensive in the world.

Foraminifera are microscopic single-celled organisms with shells (called tests), found in both modern and ancient marine environments. They either live on the sea bottom (benthic) or float in the upper water column (planktonic).

The 600+ digital volunteers have been helping to transcribe this label data so far and enabling research that can help us learn how our environment, climate and ocean have changed over 500 million years.

This project is almost complete, and with your help, we can start processing all of this data in the new year. As we process this data we look forward to sharing this data with you, and telling you of the scientific research that has thus been made possible.

If you have a few minutes to donate over the coming days, do join us on Notes from Nature to help finish off the Miniature Fossils Magnified Project. In the new year there will be new projects to join, and more outcomes to report.

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Second Expedition Studying Impact of Climate Change on Orange Sulphur Butterflies

Hello again! Thank you everyone for your help with my first expedition entering label data for the Orange Sulphur (and if you’re new to the project, welcome!). The first expedition went really well, and I’ve photographed a lot of specimens that need label data, so I’m starting a second expedition. For the second expedition, I’m using specimens from the University of Florida’s McGuire Center (It turns out they have a lot from all over the US).

The research focus remains the same as our first expedition: Orange Sulphurs have many generations each year, and their wing patterns vary seasonally across generations. The underside of their wings are dark during spring and fall, helping them warm themselves, and then lighter during summer to avoid overheating. Climate change, however, is altering the relationship between day length—which the butterflies use to determine their adult wing pattern—and the actual temperatures the butterflies will encounter. I want to know if evolution has helped the butterflies adjust to these changes (see my previous post for more details).

For this expedition, I want to share some more details on our predictions for how these butterflies might adapt to climate change by altering the seasonal variation in wing pattern. We have three main hypotheses:

  1. Producing the summer form on shorter days: The warming world effectively makes summer longer. To adjust, the butterflies could change how they respond to daylength. Normally, the butterflies produce the summer form if they experience long days as a caterpillar. In response to climate change, evolution could decrease the hours of daylight required to switch to the summer form, resulting in summer-form butterflies appearing earlier in spring and lasting later into fall.
  2. Lighter winter coloration: Instead of changing when their wing pattern changes, instead the wing patterns themselves could change, becoming lighter to be more appropriate in a warming climate. While the summer form can’t get much lighter, the spring/fall form can, so we expect to see a greater change then.
  3. Respond to temperature: Daylength indicates time of year, which was historically a better predictor of the weather weeks from now than the current temperature in most temperate climates. With climate change, however, daylength isn’t as good a predictor any more. Instead, temperature may now be a (relatively) better cue and the butterflies could have switched to using it. Some related species already use temperature instead of daylength to control similar changes. It will be hard to test this hypothesis using natural history specimens, but I’m planning additional lab experiments to test it by raising caterpillars with different temperature and light conditions to see which forms the produce.

Right: Colias eurytheme summer form (underside),

Left: Colias eurytheme spring/fall form (underside)

We could also find a combination of these predictions has occurred. Regardless, the world is warming extremely fast, so the butterflies may not be able to keep up. As another part of this project, I’m working with my advisor (Dr. Joel Kingsolver at University of North Carolina) to create a mathematical model to predict the ideal wing pattern for an Orange Sulphur butterfly depending on climate, accounting for the effect of both seasons and climate change. We plan to use this model to determine if the changes you are helping us find using museum collections are enough to keep up with climate change or if the butterflies are falling behind.

— Matthew Nielsen, University of North Carolina at Chapel Hill

Understanding A Critical Symbiosis: Nitrogen Fixing in Plants

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Atmospheric nitrogen is essential to all life, but in this form is inaccessible to all plants and animals. Much of life is limited by naturally occurring “fixation” of nitrogen, that is, rendering this element bioavailable, and this is particularly limiting for human agriculture. Nitrogen-fixing symbioses — the relationships some plants like legumes and their relatives have with nitrogen-fixing bacteria — allow legume crops to grow in poor soils without enough nitrogen to support competing plants. Understanding how this symbiosis works could reduce fertilizer use, reducing the high energy cost of fertilizer production, limiting agricultural runoff, and securing the food supply in arid parts of the globe.

One of the remarkable aspects of this globally important symbiosis is how plants able to commence it are closely clustered relatives in the Tree of Life. Although clustered, some plants within this group have the symbiosis and some don’t. It has long been thought that all plants that are part of this cluster, whether they express the symbiosis or not, share an unknown genetic mechanism that enables this plant-bacterium relationship. Researchers are slowly starting to unravel this mystery, using a combination of genomic tools and data about where these species are found.

In this expedition, we are partnering with the New York Botanical Garden to help unlock biodiversity data in plants with nitrogen-fixing symbioses as captured by museum specimens to understand the symbiosis from the genetic level to ecology. All the specimens you are helping to transcribe will also be used to generate genomic data, in order to help us further understand the underlying basis of this symbiosis. The label data are also important for helping us understand how the environment and geography have shaped this symbiosis. Your contributions will help us build one of the largest biodiversity projects yet attempted to understand the origin of this globally important plant trait.

The Delta and Crowley’s Ridge Flora (Part III)

We just completed our Plants of Arkansas: The Delta and Crowley’s Ridge Flora (Part II), which means (of course) that we are ready for Part III.  This project is a little different than our previous ones, as all the specimens included come from the University of Central Arkansas Herbarium (UCAC), and only the locality and habitat or description information need to be completed.  This means that specimens can be transcribed in record time.

I now have three graduate students who are working to discover the hidden diversity in this region of the state.  They are conducting field projects by making new collections and exploring this understudied region.  They also are using existing data in their work to fill knowledge gaps.  By assisting us in filling these data fields on the existing specimens, we can more effectively utilize these existing specimens in our research.  In other words, our new Notes from Nature expedition launch is directly related to my current laboratory research program and will assist three graduate students in their research efforts.  Thanks again for all you do, and please know how important your contributions are.

Travis D. Marsico, Curator, Arkansas State University Herbarium (STAR)

Banded Yellow Butterflies

Yellow butterflies have great significance in many cultures; some say a yellow butterfly brings guidance and is a sign of hope, while others believe it represents a new life. Whatever you might believe, it is nice to see a pretty yellow butterfly. Most yellow butterflies are in the family Pieridae, which has over 1,000 species. In this next expedition, we are looking at the pierid species Eurema elathea, the Banded Yellow butterfly. Males have delicate blackish bands spanning its yellow forewings, and in both sexes the hindwings are mostly porcelain white, giving it a distinct appearance. However, this species also has slight variations in wing color and pattern depending on where it flies; Banded Yellow butterflies have been found in the Caribbean, southern Central America, and much of South America.

Here at the McGuire Center for Lepidoptera and Biodiversity at the Florida Museum of Natural History, there is a great abundance of Eurema elathea. The information that you transcribe adds value to our ongoing research, by enhancing the data sets we use to answer questions about the history and behavior of these butterflies. We value your contributions to the scientific community, and we thank you for devoting your time and effort to help us complete these butterfly projects.

~ Stacey L. Huber, Digitization Coordinator, McGuire Center for Lepidoptera & Biodiversity, Florida Museum of Natural History

WeDigFLPlants’ Comfort Food Relatives in Florida

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Potatoes, sweet potatoes, and yams are starchy staples in many holiday meals at this time of year. We’ve wrapped together the plant families responsible for these comfort foods, Solanaceae, Convolvulaceae, and Dioscoreaceae (respectively), along with the family responsible for the Andean starch Oca (Oxalidaceae), in this new expedition. The flora of Florida contains 60 native and naturalized species from the potato family, 69 from the sweet potato family, 6 from the yam family, and 8 from the oca family. We encourage you to think about which of the four families you are seeing as you transcribe, insofar as it is easy to do so. Florida members of the yam family are all vines with heart-shaped leaves (as seen in the tile for this expedition). Florida members of the oca family are all short herbs with clover-like leaves (photo). The other two families are each other’s closest relatives and quite diverse in appearance, so there isn’t an easy way to differentiate between the two. You can watch for the most diverse Florida genera from these families though. From the potato family, you might come across Solanum (the genus that gives us potato and tomato), Physalis (the genus that gives us tomatillo), and Nicotiana (the genus that gives us tobacco). From the sweet potato family, you might come across Ipomoea (the genus that gives us sweet potato; these are the morning glories) and Cuscuta (the parasitic dodders, which look a lot like silly string). This expedition combines specimens from the herbaria at the University of West Florida, Florida State University, University of Central Florida, and University of Florida. For more info on WeDigFLPlants, visit https://biospex.org/project/wedigflplants.

Thank you for participating!

Austin Mast
Director, Florida State University’s Robert K. Godfrey Herbarium

How to Handle the Cotton Relative Specimens from the Experimental Station

You will find specimens collected by Margaret Menzel and collaborators in the Cotton Relatives in the Florida Panhandle  expedition. Margaret was a Professor of Genetics in the Department of Biological Science at Florida State University, and she is memorialized in the Margaret Menzel Award given annually by the Genetics Section of the Botanical Society of America. An example label created by Margaret is shown (photo). The meaning of some of the numbers on the label is unclear, so I looked at one of her publications on Hibiscus. In table 1 of that publication, Menzel lists alphanumeric codes similar to our example of “A63-542” as an identifier for Accession, and this is different from the HV numbers, which have a column header “Herbarium Voucher” in that table. I interpret “Accession” to be a reference to the live plant at the experimental station.  It is not clear from the publication what the PI number might be. Here is my recommendation for the transcription of this particular label. Note that I have corrected the spelling of “flouwers” in the transcription.  Thank you for participating!
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COUNTY: Palm Beach
LOCATION: Everglades Exper. Station. Seeds from Tanganyika, N. Morogoro, E. Prov.
HABITAT & DESCRIPTION: Cult. Blue-flowered. A63-542, PI292959. “May-wild-stems green, leaves divided, flowers purple”. Chromosomes: 2n + 36.
COLLECTED BY: Menzel and Wilson
COLLECTOR NUMBER: HV219
MONTH: 10-December
DAY: 12
YEAR: 1964

Austin Mast
Director, Florida State University’s Robert K. Godfrey Herbarium

 

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