What we have and what we don’t
Tomorrow begins the State of the World’s Plants and Fungi (SWPF) conference hosted by Royal Botanic Gardens, Kew. This annual conference, which typically focusses on either plants or fungi, but has this year been combined for the first time, takes stock of the world’s botanical and fungal biodiversity, its uses, and what steps need to be taken to protect it. Ahead of the conference, a special issue of the open access journal Plants, People, Planet, as well as a report based on the articles therein, were released. One of the main topics of both the report and the conference is, of course, plant and fungal collections. The related article, by lead author Alan Paton and colleagues, dives into what we have, where it’s being kept, what’s missing, and what we can do about it. This post will discuss all but the last of those topics, with a solutions-focussed part two to follow.
As an aside, perhaps we ought to first dive quickly into why these collections matter. The plant and fungal specimens that make up collections around the world are data points showing that a certain species lived in a certain place at a certain moment. Taken together, specimens can paint a picture of the abundance and distribution of a taxon and how it changes over time. Extended specimens, which are becoming more common, include not just the observable features of the sample itself, but can include photographs, ecological information, related DNA, and more, creating the potential for new uses and ways to answer scientific questions that may help in solving ecological and conservation challenges, among others.
“[N]ew approaches in the use of collections have transformed the scientific landscape in areas such as conservation, climate research, and historic disease patterns,” write the authors. “A new era of interdisciplinary research on collections is influencing the future of collections and of collecting itself.”
According to the SWPF report and Index Herbariorum, there are 3324 active herbaria in the world, containing over 392 million specimens. North America and Europe dominate these numbers, reflecting, as the report notes, “the European origin of the herbarium tradition and the fact that European herbaria hold many specimens from outside Europe gathered during the colonial expeditions of the 17th to 19th centuries.” By and large, these collections aren’t indexed by taxonomic group, making it difficult to gauge coverage. Botanic gardens and other living collections are however, and the latest numbers show just over 107,000 species representing 31% of vascular plant species.
Fungal collections comprise nearly 850,000 fungal strains in 793 culture collections, which are again concentrated in Europe and North America. With as many as 3.8 million fungal species estimated to exist, these collections represent fungal biodiversity poorly. Of the small fraction of total fungal diversity that has thus far been described, only 17% of those are cultured and publicly available for study. This is at least in part due to an isolation methodology that favours fast-growing, common fungi. New methods are currently being developed to help preserve non-culturable fungi, which may improve this situation in the future.
Seed bank holdings are difficult to pin down taxonomically, and many are geared toward agriculturally important domesticated plants, but among the botanic gardens banking wild species, 350 seed banks in 74 countries hold over 57,000 species – 17% of all seed plants – including more than 9000 that are threatened with extinction. Some of these, unfortunately, are known or suspected to be recalcitrant; that is, bearing seeds that won’t survive conventional seed bank cold storage. Around 10% of all seed plants globally are estimated to be recalcitrant, and as stated in the article, “[r]esearch is needed, both to further confirm the proportions and identities of recalcitrant species in various vegetation types; and, for high priority species, to develop alternative ex situ conservation methods, probably involving cryopreservation of excised embryos.”
Digitization of collections data has been a key move in widening the user-base of specimens. The Global Biodiversity Information Facility (GBIF), an aggregator of collections data, has linked nearly 2500 peer-reviewed research articles to data sources such as herbaria since 2015, showing the value provided by digitization efforts. A great deal of digitization remains to be done: only 21% of herbarium specimens are present in GBIF, and only 48% of those have location data given. Many smaller herbaria from biodiverse countries contain rare and irreplaceable specimens, but lack the resources to digitize collections. The greatest gaps in GBIF data occur across Asia, North and Central Africa, Amazonia, and the Canadian Arctic.
Part of the uneven coverage stems from the fact that focussed collecting efforts in a given region are often related to the specific interests of institutions and programmes, rather than the broader needs of the scientific community. “There is a tension between the general collection and digitization to fill geographic and taxonomic gaps and focused collection to provide evidence to solve particular science questions or societal challenges,” write the authors.
For a discussion of current and proposed solutions to some of these gaps, check back for part two later this week.