Jason Hale, Product Manager Data Ecosystem, takes a look at how the Museum is using a novel algorithm to overcome the challenges of cataloguing environmental DNA data.
The UK is one of the most nature-depleted countries in the world. This means that when it comes to the amount of biodiversity remaining, the UK finds itself in the bottom 10% of countries worldwide primarily due to the fact that about 70% of our land is agriculture.
As well as being a world-leading visitor attraction, the Natural History Museum also has over 300 scientists tackling some of the biggest challenges facing the world today including climate change, biodiversity loss and food security.
The Museum’s Urban Nature Project brings together a team of people looking at the challenges the UK faces with increasing urbanisation.
We’ve recently reached an exciting stage in the development of our new pond and wetland system, as part of the Urban Nature Project. We sat down with Louise Simmons, Senior Project Manager, who’s been carefully managing the process from the beginning, to hear more about what’s been happening with our brand-new pond.
The health of our planet depends on the existence of million species, the ecological networks in which they interact with one another, and the complex habitats they live in and modify. Humans are just one component of this living network and, therefore, we rely on nature for goods and services that underpin our societies, economies, health and wellbeing.
Land use change, intensive farming and hunting of wild animals all increase our exposure to parasites and pathogens. Museum collections provide vital insights into how and why these relationships are changing, and the implications these have for our health and the health of our planet.
To help us to communicate how researchers at the Museum are addressing the on-going planetary emergency, we have developed ten Research Themes. One of these themes is Biodiversity and Health which will aim to prioritise research into the intersection between biodiversity change and emerging diseases.
The UK holds some of the world’s most important natural science collections. More than 130 million specimens have been collected from around the world and are held in over 90 institutions throughout the country.
Our new gardens will be a biologically diverse hot spot for urban nature in the heart of London. One of the main features of our gardens has been the wildlife pond, which has supported a diverse range of wildlife from moorhens, aquatic plants and an important assemblage of dragonflies and damselflies.
As part of the Urban Nature Project, we’re removing the old pond liner which was at the end of its lifespan and taking the opportunity to expand the pond area so it can be home to even more urban wildlife for years to come.
Legumes are a group of plants that include soybeans, peas, chickpeas, peanuts and lentils. They are a significant source of protein, fiber, carbohydrates, and minerals in our diet and some, like the cow pea, are drought resistant.
A new paper has been published in Biodiversity Journal about a project that the digitisation team started in 2018 with the Royal Botanic Gardens Kew (project Lead) and the Royal Botanic Garden Edinburgh, to collectively digitise non-type herbarium material from the legume family This includes rosewood trees (Dalbergia), padauk trees (Pterocarpus) and the Phaseolinae subtribe that contains many of the beans cultivated for human and animal food.
This project was made possible through Department for Environment Food & Rural Affairs (DEFRA)-allocated Official Development Assistance (ODA) funding, distributed by the UK government in its “global efforts to defeat poverty, tackle instability and create prosperity in developing countries”.
ODA-listed Countries
African
Guinea, Ethiopia, Sudan, Kenya, Uganda, Tanzania, Mozambique, Malawi and Madagascar
Asian
Bangladesh, Myanmar, Nepal, New Guinea and India
Southern and Central American
Guatemala, Honduras, El Salvador, Nicaragua, Bolivia, Argentina and Brazil
The legume groups Dalbergia, Pterocarpus and Phaseolinae were chosen for digitisation to support the development of dry beans as a sustainable and resilient crop, and to aid conservation and sustainable use of rosewood and padauk trees. Some of these beans, especially cow pea and pigeon pea, are sustainable and resilient crops, as they can be grown in poor-quality soils and are drought stress resistant (Varshney et al. 2009). This makes them particularly suitable for agricultural production where the growing of other crops would be difficult.
Digitally discoverable herbarium specimens can provide important information about the distribution of individual species, as well as highlighting which species occur naturally together. While there have been collaborative efforts between herbaria in the past, these have tended to prioritise digitisation of type specimens – as the example specimens for which a species is named, types are important to identification, but as individual specimens don’t offer insights into species distribution over time. By focusing on the non-types across the world and over the last 200 years, we have released a brand-new resource to the global scientific community.
Searching for beans
This collection was digitised by creating an inventory record for each specimen, attaching images of each herbarium sheet, and then transcribing more data and georeferencing the specimens, providing an accurate locality in space and time for their collection.
We originally had four months and three members of staff to digitise over 11,000 specimens. The Covid-19 lockdown was ironically rather lucky for this project as it enabled us to have more time to transcribe and georeference all of the records.
Map showing breakdown of records by country
We were able to assign country-level data to 10,857 out of the total number of 11,222 records. We were also able to transcribe the collectors’ names from the majority of our specimen labels (10,879 out of 11,222). Only 770 out of the 2,226 individuals identified during this project collected their specimens in ODA listed countries. The highest contributors were: Richard Beddome (130 specimens), Charles Clarke (110), Hans Schlieben (98) and Nathaniel Wallich (79). The breakdown of records by ODA country can be seen in the chart below.
Pie chart showing distribution by ODA listed countries
From our data, we can see the peak decade of collection was the 1930s, with almost half (4,583 specimens or 49,43%) collected between 1900 and 1950 (Fig. 10). This peak can be attributed to three of our most prolific collectors: Arthur Kerr, John Gossweiler and Georges Le Testu, all of whom were most active in the 1930s. The oldest specimen (BM013713473) was collected by Mark Catesby (1683-1749) in the Bahamas in 1726.
Chart showing distribution of records through time
An interesting, but perhaps unsurprising, finding is that our collection is strongly male dominated. There are only two women (Caroline Whitefoord and Ynes Mexia) in the list of our top 50 plant collectors and they are not close to the most prolific collectors. We identified more women in the rest of our records, but their contribution is on average less than 25 specimens per person in the dataset consisting of more than 10,000 specimens. In contrast, the top five male collectors contributed 10% of our collection.
The oldest specimen in this collection from 1726.
Releasing Rosewoods
Both the Pterocarpus and Dalbergia genera include species that are used as expensive good quality timber that is prone to illegal logging. Many species such as Pterocarpus tinctorius are also listed on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. By releasing this new resource of information on all these plants from three of the biggest herbaria in the world is that we can share this date with the people who are taking care of biodiversity in these countries. The data can be used to could be used to identify hotspots, where the tree is naturally growing and protect these areas. These data would also allow much closer attention to be paid to areas that could be targets for illegal logging activity.
Pterocarpus tinctorius is a species of padauk tree that is listed as endangered on the IUCN Red List. Cowpea (Vigna unguiculata) is a food and animal feed crop grown in the semi-arid tropics.
Pterocarpus tinctorius is a species of padauk tree that is listed as endangered on the IUCN Red List. Cowpea (Vigna unguiculata) is a food and animal feed crop grown in the semi-arid tropics.
The ODA-listed countries are economically impoverished and disproportionally prone to be disadvantaged with the changing climate whether from flood or drought or increase in temperature. Using data to identify good, nutritious plant species that can be grown in such conditions can therefore benefit local communities, potentially reducing dependence on imports, aid and on less resilient crops.
Our pinned mayfly, stonefly and caddisfly specimens are groups of insects that have life cycles reliant on freshwater. Where these insects are plentiful, they are fantastic indicators of water quality.
Drawer of Silver-studded blue (Plebejus argus) butterflies from the Museum’s collection
A brand new scientific paper applies computer vision to over 125,000 of the Museum’s digitised Butterfly collection to understand how animals may respond to climate change.
