BioBanking at GGBN 2023: Highlights from GigaScience Press
“Extinction is forever – so our action must be immediate.”
–Sir David Attenborough, Sept 30th 2020
The fourth international Global Genome Biodiversity Network (GGBN) Conference took place in Aguascalientes, Mexico from October 17th to October 20th 2023 where it was hosted by the Universidad Autónoma de Aguascalientes. The GGBN is a global network of collections of genomic samples from across the Tree of Life, whose mission is to foster collaborations among biodiversity and biobanking repositories in order to ensure quality standards and harmonise exchange of material in accordance with national and international legislation and conventions. GigaScience Press Data Scientist Chris Armit attended the conference and reports below on some of the highlights.
Confronting the Global Decline in Biodiversity: The GGBN Perspective
Oliver Ryder (San Diego Zoo Wildlife Alliance IUCN-SSC Animal Biobanking for Conservation Specialist Group, and co-founder of Genome10K – of which we have published many genomes and standards) introduced the Biodiversity Crisis with some dizzying statistics. A study of 31,821 populations representing 5,230 species monitored across the globe showed a 69% decline in abundance. The decline is disproportionate across the globe with the megadiverse continent of Africa showing a 66% reduction in biodiversity, and Latin America and the Caribbean showing a staggering 94% reduction in biodiversity. The message is clear – we have to act now to conserve our living planet.
Conservation is a key focus of the GGBN, and this network – coordinated by the GGBN Secretariat hosted and supported by the National Museum of Natural History, Smithsonian Institution, Washington, DC – aims to provide the necessary Data Standards for BioBanked specimens in a global context.
Oliver Ryder’s keynote talk set the stage for Animal Biobanking for Conservation.
The term ‘Data Standards’ is used to describe a set of terms and controlled vocabularies designed to represent facts about a sample/voucher. An additional important concept pertinent to the focus of GGBN is the “Digital Extended Specimen”, which is a cloud of information around a vouchered specimen and which can include genomic sequence data and metabolomics data.
One Plan Approach
In his Keynote talk, Oliver Ryder highlighted the need for a common standard of good practice and information sharing. Towards this end, Oliver showcased the “One Plan Approach” which was formulated at the IUCN World Conservation Congress 2020 at its session in Marseille, France, and which “urges the Secretariat and professional societies to promote integration of in situ and ex situ conservation interventions” and “to ensure effective use of all available conservation tools”.
Of central importance for this network, are the calls on IUCN Commissions and Members to “enable and support establishment of a global network of biobanks dedicated to the achievement of global species conservation targets and operating to common standards of good practice and information sharing.”
Genetic Rescue and Cloning
Oliver Ryder further showcased a series of success stories. Foremost amongst these is genetic rescue by moving animals. Genetic rescue involves an increase in fitness from the introduction of new, unrelated individuals into small, declining populations, and we have explored this topic previously with our publication of the genome of the critically endangered helmeted honeyeater. At GGBN 2023, Oliver highlighted how genetic rescue has been successful in increasing the fitness of the Florida panther Puma concolor coryi, by moving female panthers from Texas to Florida from the mid-1990s.
Much more technically challenging is the use of cloning to increase genetic fitness in endangered species. Oliver was swift to point out that this approach has been used for the critically endangered Przewalski’s horse. The first cloned Equus przewalskii was foaled on August 6th 2020 and was named ‘Kurt’ in honour of the first Frozen Zoo creator Dr Kurt Benirschke of San Diego Zoo.
In the same year, a black-footed ferret named ‘Elizabeth Ann’ (born December 10, 2020) was the first U.S. endangered species to be cloned. Elizabeth Ann was cloned using the frozen cells from Willa, a black-footed female ferret who died in the 1980s and who had no living descendants.
Elizabeth Ann – The first cloned black-footed ferret. As a work of the U.S. federal government, the image is in the public domain.
BioBanking and the Frozen Zoo
A core focus of the GGBN conference was cryobanking of viable cells and gametes. In her talk on Biodiversity Biobanking, Jackie Mackenzie-Dodds (Natural History Museum, London) referred to the cryopreservation facilities as a “treasure trove of molecules”. Jackie pointed out that viable cell lines are the most requested resource for the Natural History Museum BioBank, where they are used for the generation of induced pluripotent stem cells (iPSCs) and chimaeras.
Another important message from the GGBN conference was the need for Open Access BioBank facilities. Towards this end, an additional incentive for researchers and curators was provided by Mudzuli Mavhunga of Biodiversity Biobanks South Africa (South African National Biodiversity Institute, Pretoria). Mudzuli highlighted that, if a South African BioBank is awarded the status of Open Access, then it is eligible for resource allocations through Biodiversity Biobanks South Africa (BBSA), which is a great asset for a collection facility.
Mudzuli Mavhunga highlighted advantages for BioBanks in ensuring that genomic collections are Open Access.
Scalability of Cloning
So is cloning from frozen somatic cell lines a scalable approach? Ben Novak of Revive & Restore (Sausalito, California), in his talk entitled “Important Considerations for Biobanking for Genetic Rescue of Endangered Species”, highlighted the example of passerines (perching birds) where programmed DNA loss is observed in some species. In passerines such as the zebra finch (Taeniopygia guttata), there is a germ-line-restricted chromosome – known as an accessory chromosome – that is present in the oocytes and spermatocytes, and is subsequently lost during male meiosis. This germ-line restricted chromosome is unusual in that it is represented exclusively in the germ cells, and is absent from somatic cells of the bone marrow and skin and liver fibroblasts.
DNA elimination is observed in many vertebrate and invertebrate species, and can occur through chromosome breakage and selective loss of chromosome regions and/or the elimination of individual chromosomes. However, this phenomenon, if observed in somatic tissues, can severely impact on the ability to generate functioning iPSCs from frozen cell lines.
Ben Novak offered insight into the genetic rescue toolkit, and some of the challenges for conservation.
As Ben explained, a key consideration for cryobanking is “which tissues to save?”. The inclusion of an additional cytogenetics step, to ensure a cell line is chosen where the chromosomal integrity is maintained, is one means of addressing the challenge of germ-line-restricted chromosomes in the cryopreservation of endangered species. The alternative is to cryopreserve reproductive tissues.
Cryopreservation for BioBanking of Gametes and Reproductive Tissues
On the subject of cryopreservation of reproductive tissues, invaluable insights were provided by Tullis Matson of Nature’s SAFE, whose mission is to combat extinction by collecting, indefinitely storing and regenerating reproductive cells and cell lines from endangered animal species.
Tullis has expertise in artificial insemination of rare equine breeds, including the critically endangered Suffolk Punch for which there are only 300 individuals in the world and only 80 breeding females. Tullis has created Nature’s SAFE with the intention of applying this know-how of rare equine breeds to endangered mammalian species, and has been on field trips to cryopreserve sperm from elephants in South Africa. An important message was that the samples that were obtained in South Africa stay in South Africa, which is both an ethical and legal obligation (see Sharing of Genomic Collections under the Nagoya Protocol below).
Tullis additionally highlighted the importance of harvesting epididymal samples, and the role of Nature’s SAFE in cryopreservation of ovarian tissue from the pied tamarin (Saguinus bicolor, critically endangered), the lar gibbon (Hylobates lar, endangered), and the cheetah (Acinonyx jubatus, vulnerable). As Tullis explained, “working with leading reproductive scientists and cryobiologists, we use state-of-the-art methods to preserve cells in a way that maintains viability, allowing them to be thawed and used to establish pregnancies, restoring endangered animal species”.
From Fieldwork to BioBank
Whereas there was clear focus on BioBanking at the GGBN conference, I was additionally interested to hear that GGBN standards are useful from a rewilding perspective. Beth Kaplin (Center of Excellence in Biodiversity and Natural Resource Management, University of Rwanda) offered some invaluable insights on this topic, and highlighted that environmental DNA (eDNA) and environmental specimen metadata is used for decision making in projects such as the rewilding of Akagera National Park. In this project – which is funded by the National Geographic Society – eDNA sampling of sediment cores and sample surface sediments are combined with natural history observations, and used to understand biodiversity patterns and assist park management in their plan for reintroductions.
Beth Kaplin highlighted the infrastructure challenges associated with rewilding in Rwanda. Image reproduced from here.
Sharing of Genomic Collections under the Nagoya Protocol: Recognition of Indigenous Peoples and Local Communities
The Nagoya Protocol on Access and Benefit-sharing became effective in 2014. It is an international agreement which aims at sharing the benefits arising from the utilisation of genetic resources in a fair and equitable way. One of the key features of the Nagoya Protocol agreement is that a permit is required for gathering a specimen. From a GGBN perspective, it is a requirement to share this information with GGBN, where it is stored in the Darwin Core metadata associated with a sample.
As an illustrative example, Jocelyn Cheé-Santiago (Universidad Autónoma de Aguascalientes) focused on the Nagoya Protocol as it relates to Mexico and explained, “you need to get a permit of collect”. One of the reasons for a permit is to ensure the recognition of the collective property of indigenous lands, and to ensure that allegations of biopiracy are excluded from genomic collections. As Jocelyn explained, “the heart of the Nagoya protocol is community consent – informed consent from indigenous people”.
Jocelyn Cheé-Santiago reported on the implementation of the Nagoya Protocol in Mexico.
This sentiment was echoed by Guadalupe Yesenia Hernández Márquez (International Indigenous Forum on Biodiversity and Ecosystem Services IIFBES, Mexico), who highlighted that the Nagoya Protocol is “the only legally binding document that recognises community protocols”. A corollary of this is that it is important to have community involvement and community consent prior to commencing fieldwork.
This is an important message for GGBN and for the wider BioBanking community.
Thank you to the conference organisers Gilberto Ocampo (Universidad Autónoma de Aguascalientes), Katie Barker (GGBN/Smithsonian Institution, National Museum of Natural History), and Jonas Astrin (Leibniz Institute for the Analysis of Biodiversity Change) for a wonderful selection of talks.
Many additional talks from GGBN 2023 are included in the following playlist.
We look forward to the next GGBN Conference in Kirstenbosch National Botanical Garden, Cape Town, South Africa in 2025.
