CryoArks Biobank and COVID-19

Written by Andrew Kitchener, Principal Curator of Vertebrates, National Museums Scotland.

Biobanks may sound a bit dull when compared to shelves teeming with boxes filled with fascinating skeletons, or cabinets stuffed with colourful skins, beautiful eggs or pinned insects. Serried ranks of anonymous freezers, enhanced with the odd fridge magnet, could make your heart sink, but peep inside the biobanks’ databases and you will see an amazing array of biodiversity. 

CryoArks Biobank at National Museums Scotland ©National Museums Scotland

At National Museums Scotland we host one of the main hubs of the CryoArks Biobank initiative alongside our partners at the Royal Zoological Society of Scotland, who also host a hub of the European Association of Zoos and Aquaria Biobank, and the Natural History Museum in London. CryoArks is a project led by Professor Mike Bruford of Cardiff University and funded by the Biotechnology and Biological Sciences Research Council to establish zoological biobanking in the UK. As well as the -80o freezer infrastructure to store the tissue samples long term, CryoArks is developing an online database that will allow researchers to find out what genetic resources are available in the CryoArks Biobank hubs and in member institutions. With the advent of the Nagoya Protocol on Access and Benefits Sharing in 2014, access to genetic samples from species from range countries is more challenging. Therefore, it is vital that we make the best use of the samples already available in the UK and make these freely available to support research, much of which may benefit the conservation of endangered species worldwide. 

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CryoArks – Discover The UK’s First Zoological Biobank

Written by Andrew Kitchener, Principal Curator of Vertebrates, National Museums Scotland.

Many of us have probably been approached by eager PhD students and other researchers who want to snip a bit off those specimens or drill a few holes in others. As curators we start to feel somewhat uncomfortable about seeing our precious collections sliced and diced, and yet we are also keen to discover more about the genetic content of our specimens for their own sake. This is partly because collectively we can contribute to studies that benefit wild populations of species, including the conservation biology of many endangered species and the possibility of rewilding extirpated species. You may also have a chest freezer bursting with grip-seal bags or plastic tubes filled with tissue samples collected from specimens you have acquired, but you’ve no idea what to do with them, but you know they will be useful one day. Or maybe you have a freezer full of specimens you want to get rid of. CryoArks is a new initiative that just might help you to solve all these problems.

Sorting through lemur muscle samples at National Museums Scotland © National Museums Scotland

CryoArks is a BBSRC-funded project led by Professor Mike Bruford at Cardiff University, which has established the UK’s first comprehensive zoological biobank for research and conservation. CryoArks is a consortium of museums, zoos, academic institutions and biobanks, which is working together to establish common standards and working practices to store tissue and DNA samples and make them available on a common web portal, so that researchers and conservation biologists will be able to find out what is available for their research. This will help cut down on the sampling of our permanent collections by giving researchers something else to sink their scalpels into. CryoArks has two main sample storage hubs – at the Natural History Museum in London and at National Museums Scotland in Edinburgh – that currently house more than 65,000 samples, but we have room for almost a quarter of a million. The Royal Zoological Society of Scotland is also a joint CryoArks and European Association of Zoos and Aquaria biobank storage hub, bringing the zoo and non-zoo biobank communities together.

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Meet the NatSCA Committee – Kirsty Lloyd

Written by Kirsty Lloyd, BBSRC CryoArks Technician at the Natural History Museum, London.

What is your role on the NatSCA Committee?

I have recently become a member of the NatSCA committee after attending their conferences and events for several years.

Thus far I have taken on the role of tracking and supporting collections at risk. A natural sciences collection provides a perpetual physical snapshot of the natural world and holds important information which can help us better understand our planet today. However, this valuable resource is often the first to experience the strain of funding cuts, staff shortages and redundancies. Collections in long-term storage, especially those that exist outside of the public eye, are frequently underutilized and therefore undervalued.

NatSCA is trying to keep track of threats to collections and offer our support to those in need; with the intention of increasing awareness and acknowledgement of the value of natural sciences collection and the people with the skills to care for them. If you know of any collections that are at risk from staff loss or collection disposal, please get in touch at advocacy@natsca.org.

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Bill Pettit Memorial Fund: Discovery Collections Project

The Bill Pettit Memorial Award was set up a few years ago by NatSCA to support projects including the conservation, access, and use of natural science collections. One of the recent projects we have been able to help with was the curation of some amazing specimens from the voyage of the Discovery. Hear more about the project from Tammy below.

David Gelsthorpe

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In early 2013 we set about organising the task to begin with the curation of the largest, most recent and least organised of the three collections – that of the ECOMAR collection. The start of the ECOMAR project coincided with commissioning of the new UK Royal Research Ship James Cook officially named by the Princess Royal on 6 February 2007. The first ECOMAR cruise departed from Southampton on 13 July 2007. The ECOMAR project was designed to investigate the Charlie Gibbs Fracture Zone area which lies approximately mid-way between Iceland and the Azores. Four super stations were defined (two north of the Charlie Gibbs Fracture Zone and two to the south), all had the same bottom depth (2500m) and were revisited during voyages by the R.R.S. James Cook and the R.R.S. Discovery during the years 2007–2010 to replicate sampling, time-series investigations and flux studies.

The Discovery Collections have no full-time curatorial post and we rely on the goodwill and interest of students and other volunteers (including scientific visitors and work experience volunteers) to help with cataloguing, labelling, respiriting, and general curatorial jobs. The samples, though incredibly valuable should be considered at risk. I look after the collections in as much that I manage the visitors to the collections, host students, and manage public enquiries, visits and displays of the specimens. I am also a taxonomist employed to conduct research, describing new species and studying the ecology of the deep-sea benthic fauna. I was employed for four years to work on the ECOMAR program to describe the ecology of the scavenging fauna of the area. I therefore had a particular interest in the curation of this collection.

We employed Amanda Serpell-Stevens, to work on this project, but we had funds for only 8 weeks of her time. Thus the project was reduced from cataloguing the three large collections to just one. When Amanda’s contract ended there was still much reshelving and reordering of the material to be carried out which was carried out on an ad hoc basis by myself, a retired member of staff, Mike Thurston, and Amanda who returned on a voluntary basis to continue work on the project.

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The project began by working shelf by shelf to curate and to catalogue (in paper record) what was held including location and size of each jar, and to change containers for those specimens that were in plastic containers or inappropriate sized jars. The preservative was also replaced in most of the jars and a new label produced for each specimen, as many were poorly labelled. This curation and cataloguing process took the majority of the 8 weeks, with just enough time remaining to enter the data into Excel.

With the availability of a digital catalogue the task of reorganising the lots into taxonomic order was greatly eased. This meant adjustment of shelf heights to incorporate the various sizes of tubs and jars (some of the lots are 20 litre tubs full of holothurian specimens of a single species), and removing all the specimens in turn, which were then replaced first by taxonomic order then by station order using Excel to sort the data. The spreadsheet was updated with the new locations of the specimens as we progressed. The final part of the process involved cross referencing the specimens with the newly published papers and updating the names where they had changed (on both the specimen labels and in the spreadsheet).

There were numerous new species described during the ECOMAR project, which meant further problems in allocating the correct new name to specimens in the collections variously named as e.g. Peniagone sp. nov ‘pink’. While holotypes have been registered in the NHM, London, the rest of the material needs updating to current knowledge, a process which is often neglected, despite it being referenced in the many new publications resulting from the project.

It is very satisfying to have the ECOMAR collection properly curated and to know that I can locate any specimen needed easily. In total we curated, relabelled and catalogued a total of 1300 lots comprised of 1148 smaller jars, 88 tubs (between 5 and 20 litres) and 64 loan specimens. We plan to publish a detailed analysis of this work for the NatSCA journal, including a list of available species, and will make the catalogue available online when time and funding allow. In the meantime interested parties can contact Tammy Horton (tammy.horton@noc.ac.uk) for a copy.

Dr Tammy Horton
Ocean Biogeochemistry and Ecosystems
National Oceanography Centre,
Waterfront Campus,
European Way, Southampton SO14 3ZH
UK

Collecting biological specimens essential to science and conservation

A letter signed by more than 100 biologists and biodiversity researchers,  published online in Science today (Science 23 May 2014: Vol. 344 no. 6186 pp. 814-815 DOI:10.1126/science.344.6186.814), states why collecting plant and animal specimens is essential for scientific studies and conservation and does not, as some critics of the practice have suggested, play a significant role in species extinctions.

Beetle collection. Image by Paolo Viscardi

The letter is a response to an April 18 Perspectives article in Science arguing that alternative methods of documentation—such as high-resolution photography, audio recordings and nonlethal tissue sampling for DNA analysis—make the field collection of animal and plant specimens unnecessary. As most natural sciences collections professionals are fully aware, this is simply not the case.

“None of the suggested alternatives to collecting specimens can be used to reliably identify or describe animals and plants,” said Cody Thompson, mammal collections manager and assistant research scientist at the U-M Museum of Zoology.

“Moreover, identification often is not the most important reason to collect specimens. Studies that look at the evolution of animal and plant forms through time are impossible without whole specimens. Preserved specimens also provide verifiable data points for monitoring long-term changes in species health and distribution.”

In addition, specimens from museum collections and their associated data are essential for making informed decisions about species management and conservation now and in the future, the authors state.

“Photographs and audio recordings can’t tell you anything about such things as a species’ diet, how and where it breeds, how quickly it grows, or its lifespan—information that’s critical to assessing extinction risk,” said Luiz Rocha of the California Academy of Sciences, who organized the response to the Science article.

And contrary to statements made in the April 18 Science article titled “Avoiding (Re)extinction,” collecting biological specimens does not play a significant role in species extinctions, according to the rebuttal authors.

In the April article, Arizona State University’s Ben Minteer and three co-authors cite several examples of species extinctions and suggest that the events were linked to overzealous museum collectors.

Not so, according to authors of the rebuttal letter, who reviewed the evidence and found that none of the cited extinctions—including the disappearance of flightless great auks in Iceland and Mexican elf owls on Socorro Island, Mexico—can be attributed to scientific collecting.

Millions of great auks were harvested for food, oil and feathers over the millennia, and only about 102 exist in scientific collections. Mexican elf owls were common when specimens were collected between 1896 and 1932, and the most likely reasons for extinction around 1970 were habitat degradation and predation by invasive species.

At the same time, Minteer and his colleagues failed to point out any of the valuable services that museum biological collections have provided over the decades, according to the rebuttal authors.

Both historical and new collections played a key role in understanding the spread of the chytrid fungus infection, one of the greatest current global threats to amphibians. The decision to ban DDT and other environmental pollutants was based on the discovery of thinning bird eggshells collected over an extended period. And the declining body size of animals, one of the negative effects of climate change, was discovered using body-size data from museum specimens.

Egg collections like this helped identify the harm done by DDT. Image by Paolo Viscardi

In other cases, genetic data from decades-old scientific specimens has even been used to “de-extinct” species. One of these, the Vegas Valley leopard frog, was thought to have gone extinct in the wake of Las Vegas development. However, a study published in 2011 compared the genetics of specimens from the extinct population to individuals from surviving populations of similar-looking frogs elsewhere in the Southwest and found them to be the same species.

These types of discoveries are “the hallmark of biological collections: They are often used in ways that the original collector never imagined.” And with the continuing emergence of new technologies, this potential only grows.

That potential, combined with the increasing number of threats species face and the need to understand them, suggests that the need to collect specimens—and to share the information they hold—has never been greater.

In their April article, Minteer and his colleagues erroneously portray scientific collecting in a negative light that distracts from the primary causes of modern extinctions: habitat degradation and loss, unsustainable harvesting and invasive species.

“Halting collection of animal and plant specimens by scientists would be detrimental not only to our understanding of Earth’s diverse biota and its biological processes, but also for conservation and management efforts,” said Diarmaid O’Foighil, director of the U-M Museum of Zoology and a co-author of the rebuttal letter.

“That detriment in understanding would only increase with time because having museum specimens available for future generations of scientists will allow their study using research methodologies that have yet to be invented.”

A pre-publication pdf version of the letter can be read here.