Natural History Collections In The Digital Age. An image of the entrance hall of the Natural History Museum in London. It is a large open space with the skeleton of a whale suspended from the ceiling.

Natural history collections in the digital age


Dr Gunnell’s work focuses on the collection, management and preservation of vertebrate fossils while his research aims to understand the origin and diversification of modern mammalian groups by study of their fossil record. Dr Boyer’s work focusing on the evolution of primates uses the fossil record as a key resource for understanding the interplay between form and function in evolutionary contexts. He founded MorphoSource and manages its development and governance.

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In this episode, we’re going to be talking about Dr Gregg Gunnell’s research on natural history collections in the digital age.


So, for many, a trip to a natural history museum is a childhood rite of passage – and for some, it inspires an interest that lasts a lifetime. Dr Gregg Gunnell is director of the Division of Fossil Primates at the Duke Lemur Center in Durham, North Carolina. He is passionate on the subject of natural history and his work highlights the importance of maintaining existing collections. Similarly enthusiastic about knowledge sharing, Dr Doug Boyer, a colleague of Dr Gunnell’s in the Department of Evolutionary Anthropology at Duke, has developed MorphoSource, a web archive for storing and accessing 3D models of specimens. This archive makes natural history collections accessible for people across the globe.


Our planet is over 4.5 billion years old. Life has existed on Earth for about 4 billion of those years, starting out in the form of single-celled organisms and evolving from there to where we are today. The earliest appearance of our species, Homo sapiens, is understood to have been about 200 thousand years ago, and ‘modern humans’ (who are distinct from others of their species by their more complex and ‘intelligent’ behaviours) appeared more recently.


Despite being relative newcomers to life on Earth, unlike any other species, we have managed to gain an understanding of the planet’s natural history, even from long before our existence. The skeletons, shells, and outlines of ancient animals from millions of years in the past have been preserved as fossils. Just as the earth preserves remains of deceased animals for eons, society strives to immortalise collected specimens for eternity in natural history collections. These collections provide us with an insight into past and present biodiversity, acting as snapshots of life on Earth, and can be used to inform future conservation of species and diversity as we know it today.


Firstly, let’s look at recording the past.

Fossilisation is the Earth’s natural method of preserving the remains of organisms that once lived on its surface. These fossilised remains provide us with detailed information about species that are now long-extinct. For example, a fossil of an animal can tell us where and when that animal lived, and how it lived by its morphology (its shape): by examining its teeth, we can identify what it ate and by examining its bone structure we can determine how it moved and to which present species it may be related. We can also identify closely related species through examining teeth and other skeletal elements, as recently diverged species share similar dental and body patterns. This can then help us to identify where certain species originated and how they have evolved over time, and aid in providing us with an understanding of the environmental conditions of the past.


Like the species that inhabit it, planet Earth has evolved and changed tremendously over billions of years, and studying fossils helps us to piece together and understand this journey. For example, if a fossil of a species is found in southern Africa, and another identified to be from the same period is found in South America, this tells us that at that time, these two continents were most probably positioned close together.


Now, let’s move on to look at natural history collection.

The physical and chemical conditions must be just right for the Earth to preserve a deceased animal until it is found by a palaeontologist, so much so that only a vanishing fraction of all organisms become fossils. Similarly, museums have unforgivingly precise protocols for preserving specimens in natural history collections: each type of specimen has a different protocol depending on its composition and what is valuable about it. Such specimens can range from plants to animals to fungi, and contain valuable physical data, including DNA and the species’ physical morphology. This information is vital for understanding various ecosystems and how they have been affected by certain events, which will then help us in conserving and protecting these ecosystems and species, should similar events occur again.


These physical specimens are extremely valuable to natural history research and are kept in museums and universities around the world, providing the public, students, and researchers alike with an insight into past and present biodiversity.


Our focal example is the Division of Fossil Primates (DFP) at the Duke Lemur Center, headed up by Dr Gregg Gunnell. The collection contains over 35,000 specimens of primate and other vertebrate fossils, principally from three crucial places and time slices in the world. These places include: 37 to 20 million-year-old samples from North Africa (ie, Egypt) where fossil evidence documents the origin and diversification of anthropoid primates (today’s monkeys, apes and humans); 12 to 13 million-year-old rocks in Colombia where the diversification of New World Monkeys can be documented and studied; and subfossil samples from the island of Madagascar that document the devastating impact of human arrival on the island some 3,000 years ago. This range of specimens is carefully conserved and is available for researchers and students to access. In addition, DFP have an ongoing fieldwork programme in place to collect additional specimens from Egypt, Madagascar, Indonesia and Wyoming.


Each collection like the one at DFP is unique and therefore critical for our understanding. The catch 22 of uniqueness, is that it is very difficult for a lot of scientists or the public to benefit from the information they contain. Access and use must be restricted and monitored to protect the specimens. Researchers might have to travel thousands of miles to see them. This means we don’t have a good way of knowing how valuable the material ‘would be’ if more people could afford to come and study it.


For many research purposes, there are no easy solutions here: accessing physical specimens is essential for sequencing a copy of the species’ DNA, or documenting its pelage characteristics. However, some research questions can actually be answered more effectively through study of a ‘virtual specimen’: a computer file that emulates the physical specimen in 3D on your computer screen in a way that lets you take measurements of the size and shape of anatomical structures, and even see inside it with microscopic resolution and macroscopic clarity. Though digitisation does not mean we can discard the physical specimens (they serve as the gold-standard of the digital information), it does mean the specimens can become more widely accessible. The push to 3D digitise natural history collections is catalysing a profound change in the methods and rate of study. Frankly, the blockades to access mentioned have been crippling. One upshot is that specimens from different museum collections could rarely, if ever, be directly compared except through photographs and simple measurements.


Now let’s talk about the position of natural history in the digital world.

The world is more connected now than it has ever been, with knowledge and information available and able to be shared rapidly and easily. Because of this, digitising and digitally serving natural history collections stands to have a transformative impact on natural sciences. Here, DFP is taking the lead. Dr Doug Boyer, a colleague of Dr Gunnell, is the primary developer of MorphoSource, a web archive that allows for the storage and sharing of both raw x-ray CT-scan data and 3D models of specimens from DFP and elsewhere. Users can study the physical traits of an organism without physical access to the specimen itself. And because most of the specimens are digitised by Micro-CT scanning technology, not only the surface morphology but also the internal anatomy of specimens can be analysed and studied. In addition to digitising the DFP collection, MorphoSource also allows researchers and other museums to share their own data, including any 3D data representing a museum vouchered natural history object even if it is from a living animal, or an archaeological artifact.


Such 3D data is already collected in research, but is rarely published or made available; MorphoSource provides a data-sharing platform which allows results from studies to be verified or replicated. It can be thought of as a virtual museum that houses 3D versions of all the world’s most important fossils in a single place. Over 150 different museums from around the world are represented by specimens on MorphoSource.


And finally, we’re going to look at protecting the future.

Natural history collections are extremely important in preserving and understanding past and present biodiversity; they give us an insight into the structure of past biological communities and how they have changed over time. They allow researchers to identify how communities have responded to past events, giving a valuable insight into possible outcomes for such events in the future and ensuring that preparations can be made to protect biodiversity. Integrating global datasets from collections around the world provides valuable educational material, opens new opportunities to people worldwide and advances our understanding of species and biodiversity. DFP, MorphoSource and other natural history collections are committed to aiding the global research effort in this area.


But why should we care about biodiversity – what does it matter if species go extinct? Aren’t they going extinct all of the time?

Biodiversity is really the end-product of a constantly changing and adjusting evolutionary process – some extinction is natural but it happens within the context of the whole community that is evolving as one enormous and complex entity. Our natural history collections and the study of the natural world have begun to reveal the complex interplay between species and the important roles that species play both in regard to each other and as part of the whole. Natural history collections document that this process of inter-dependence has been on-going virtually since life first appeared on the planet. Importantly, though, the unnatural loss of species (i.e., not normal extinction but that caused by outside influences) resets the delicate balance and may have cataclysmic results (witness the Permo-Triassic extinction for example where nearly 95% of all life was wiped out). This reset the direction of future evolutionary development in a much different way than previous to the event. We would not even understand this concept without natural history collections.


Building on that, study of natural history confirms that by even the most conservative estimates, human activity has accelerated the pace of extinction by 50–1000 fold over ‘background extinction’ (see Ceballos et al 2015 in PNAS, or Johnson et al 2017 in Science). As Dr Gunnell succinctly puts it: ‘Humans rely on the productivity of Earth’s ecosystems and we destroy them at our own peril without reliable knowledge of which losses will trigger trophic collapses.’

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