The Many Lives of Herbaria

The many lives of herbaria

The Conservatory and Botanical Garden of Geneva holds a herbarium of unmatched richness, the result of a botanical tradition dating to the end of the eighteenth century. This dynamic collection, ever in motion, is used daily by our researchers and those from around the world to study, understand and protect the world of plants and fungi.

The placing of dried plants in herbaria is a practice that goes back to the 16th century. It quickly became evident that it is the simplest way to study them without the constraints of time or space. During the era of great explo- ration, the practice became widespread, having as its ambition a truly titanic endeavor: describing and classifying the world of plants and mushrooms in its entirety. This is the first life of herbaria.

Owing to technological advances, herbaria reveal themselves to hold new information which earlier botanists certainly could not have imagined. It is these many lives of herbaria which this exhibition offers for your discovery.

Un musée Impressum Ville de Genève www.cjb-geneve.ch

Organisation Conservatoire et Jardin botaniques de la Ville de Genève Director Pierre-André Loizeau Exhibitions comitee Danièle Fischer-Huelin, Nicolas Freyre, Didier Roguet Les multiples Head of exhibitions & events Didier Roguet vies des herbiers Exhibition curators Yamama Naciri and Laurent200 Gautier Scenography Laurent Pavy Logistics Cédric Forfait, Les Ateliers Casaï and Makro Art for the outdoor arrangements Design Matthieu Berthod Publicity Gisèle Visinand Scientific communication Magali Stittelman, Rhéa Garratt Documentation Rhéa Garratt Drawings Maud Oïhenart Giant herbarium specimen Florence Buholzer Videos Romain Dewaele Texts Philippe Clerc, Laurent Gautier, Yamama Naciri, Fred Stauffer Translation Daniel Hoffman (panels, booklet), Rhéa Garratt (discovery book) Image credits Philippe Clerc, Pierre-Emmanuel Du Pasquier, Lucie Garnier, Rhéa Garratt, Laurent Gautier, Daniel Jeanmonod, Pete Lowry, Fred Stauffer, Ulf Swenson David Wagnières, Mélanie Zogheb In-house collaboration Paola Adoboli, Véronique Besse, Pierre Boillat, Martin Callmander, Véronique Compagnon, Gregor Dalliard, Sylvie Dunant, Cédric Forfait, Nicolas Fumeaux, Fabrice Golay, Lydie Homberg, Tina Jaton, Marty Kohler, Raoul Palese, Mathias Perrin, Michelle Price, Macarena Ranos-Lopez, Fred Stauffer, Fabienne Thonney, Angela Wangeler, and all collaborators of CJBG. Thanks Bioscope (University of Geneva, Pierre-Emmanuel Du Pasquier, Daniel Jeanmonod

Un musée Ville de Genève

www.cjb-geneve.ch

Célébration Exposition du bicentenaire Les29 multiples 03 17-31 12 18 200 1817 - 2017 vieswww.cjb-geneve.ch des herbiers

Célébration Exposition du bicentenaire 29 03 17-31 12 18 1817 - 2017 www.cjb-geneve.ch Taxonomy, the first life of herbaria

The invention of the herbarium as an object is attributed to Luca Ghini (1490- 1556), a teacher of botany in Bologna who was the first to systematize a drying technique making possible the preservation of plant specimens and their study at any time and place. Later, as the practice spread, the herbarium became a complex installation in which collected specimens are gathered, organized and archived in such a way as to make them available to scien- tists. In our everyday relationship to plants and mushrooms, the herbarium thus represents the essential archive for identifying and classifying plant and fungal diversity.

1. Preserving. Drying and pressing the plants allows for their preservation, in principle forever, if the con- ditions for conservation are good: stable humidity and temperature (H: 40-60%; T: 18-20°C), limited exposure to light, and protective measures against pests.

2. Gathering. The herbarium is a veritable plant library and database which is constantly being enriched with new specimens collected by our researchers, or acquired through gifts, purchases and exchanges. This allows botanists to find the information they need in a single place.

3. Organizing. In a herbarium, specimens are classified according to family, genus, and species, so as to make them easily retrievable.

4. Archiving. The herbarium preserves samples collected during very different periods. The old specimens are never displaced by newer ones. The specimens are indeed the archives of botanists: they prove the existence of a given species at a particular place at a given moment.

5. Making the collection available. Even if the plants themselves are not alive, the herbarium is all the more a living tool in that it is a dynamic collection in constant use. The taxonomic expertise of the researchers of the CJBG and its scientific visitors helps to improve the identification of the specimens and refine their classification.

Taxonomy, the first life of herbaria

A vast network for inventorying biodiversity

The 350 million specimens preserved in the some 3000 herbaria of the world furnish the raw material for the work of botanists and mycologists in their endeavor to inventory biodiversity. The Geneva herbarium, with its 6 million specimens, stands among the ten most important herbaria in this network.

New species and type-specimens

Every day the scientific community describes new species, especially arising from the very rich tropics. Since 2010, more than 80 new species have been described by the researchers of the CJBG, and others are still hidden in the herbarium, waiting to be identified. Every description of a new species requires selecting a herbarium specimen, the type, which forever becomes the specimen of reference for the species. To be valid, a species description needs to be published in a scientific journal, and the type specimen as well as the herbarium where it is deposited must be cited. The high number of type specimens in the Geneva herbarium makes it particularly rich.

Many specimens per species

A species exists in nature as an ensem- ble of individuals which aren’t all exactly identical to the type. To understand what a species is, is it is important to apprehend this variation and study as many specimens as possible, ideally from diverse sites. Each species of plant or mushroom therefore is rep- resented in the herbarium by a more or less large number of specimens, which serve as well to assess its geographic distribution. Taxonomy, the first life of herbaria

Herbarium specimens and botanical works

Herbarium specimens contain the necessary information for elaborating botanical works, be they linked to a given territory (checklists, floras, atlases, Red Lists), or to a group of species (monographs, articles).

A checklist, or catalog, is a list of species for a given territory.

A flora refers to a list of species augmented with species descriptions and identification keys.

A Red List assesses the threats faced by the species of a given territory. Cri- teria established by the International Union for the Conservation of Nature (IUCN) are often used to determine threat levels.

An atlas provides distribution maps for the species of a given territory.

A monograph is a detailed study of a group of plants (for example, a genus or family). It is often during the preparation of monographs that new species are discovered in herbaria.

Herbarium specimens cited in monographs and floras

This specimen was collected in Crete by Franz Wil- helm Sieber (1789-1844) in 1826, then sent to the De Candolle herbarium identified as Campanula nutans. Alphonse De Candolle (1806-1893) discovered that it was actually a species new to science. He decided to name it Symphyandra cretica and wrote this name on the specimen (arrow).

He descibed the species in his Monographie des Cam- panulées published in 1830 (left, arrow), citing Sieber’s specimen as type.

Half a century later, Pierre-Edmond Boissier (1810- 1885), in the third volume of his Flora Orientalis published in 1875, cites the species (right, arrow), specif- ically refering to De Candolle’s monograph and citing Sieber’s specimen. Digitalization: the virtual life of herbaria

The dilemma of the curator: making the herbarium available while preserving the collection

Taxonomists need to be able to consult as large a number of specimens as possible, often preserved in several herbaria around the world. As such, either the botanist has to travel (every year we receive more than a hundred scientific visitors) or the specimens have to be sent to her or him as a loan (we continuously have tens of thousands of specimens on loan throughout the world). Two innovations together have revolutionized access to herbaria: digital imag- ery and the Internet. For flowering plants, it is estimated that in 75% of the cases a good digital image is sufficient for a taxonomist, and the specimen itself can thus remain protected from the risks of transit. The worldwide effort by some 300 herbaria in 70 countries has already put images of more than 2 million type specimens on the Web.

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What does one see on a digital image?

A digital image is taken with the help of an upside-down scanner or a high-defi- nition digital camera. Images of herbarium specimens are taken at a resolution of 600 dpi, equaling 240 dots per centimeter, giving a total of some 86 million pixels per image. A user on the Internet can thus zoom in and view a specimen at a magnification of up to 10x. In this way, certain parts, often miniscule, can be studied directly from the images.

Different zooms of a digitalized herbarium specimen. Digitalization: the virtual life of herbaria

The digital repatriation of herbarium specimens

Because of the eminent history of our collections, we hold here in Geneva reference specimens from every continent. It is our obligation to make sure these specimens are available to everyone, particularly to the botanists in the countries from where they were collected. Our herbarium indeed is consulted from a distance by botanists all over the world, thanks to the virtual catalog of the collections which is continuously available online and free of charge.

Origins of the digital images requests

Priorities

The digitalization of our entire, immense herbarium, with some 6 million specimens, is beyond the capacity of the CJBG. As a priority, the type specimens have been digitalized, as well as the historic collections (which are not sent on loan). Between 2004 and 2014, funding from the Andrew W. Mellon Foundation allowed us to digitalize ca. 136,000 specimens, including all the types in the general collection and half of the historic de Candolle herbarium. A current grant from the Franklinia Foundation is allowing us to complete the digitalization of the de Candolle herbarium, as well as the critical Boissier’s Flore d’Orient herbarium and the pre-Linnaean herbarium, which holds our oldest specimens. Molecules: the secret life of herbaria

Even after drying, herbarium specimens hold a veritable treasure: the DNA molecules carrying the information needed by organisms to grow and reproduce. DNA consists of very long sequences of 4 chemical bases symbolized by A, C, G, and T. DNA analysis is a technique which is increasingly used by taxonomists to classify species, and detect new ones. By comparing the DNA of different specimens, we can reveal changes appearing through evolution (mutations) which provide valuable indicators for identifying and classifying species, and recon- structing their evolutionary past and hereditary relationships. DNA is not the only molecule preserved in specimens. Many other compounds are also preserved, which modern techniques can characterize.

Progression of requests for sampling for DNA analysis

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04 2003 20 2005 2006 2007 2008 2 2009 2010 3 2011 201 201 2014 2015

Evolution of requests regarding CJBG herbarium specimens fragments for DNA sequencing

Horizontal window The chemistry of herbaria: following species by traces

Lichens—mushrooms living in symbiosis with algae—produce more than 1,000 unique chemical compounds which are preserved in the specimens of the herbarium. These substances protect algae from UV light and predators, among other things. As some species have characteristic array of substances, taxonomists can use these to identify them. The compounds are identified using thin-layered chromatography, which entails separating them on a plate layered with silica immersed in a bath of solvent. The lichenous substances are then identified by their position on the plate, their color, and their ability to absorb UV light.

Chromatography developing chamber: lichen substances migrate vertically by capillarity on the silica gel pre-coated TLC plates and get separated based on their affinity either with the silica gel or with the solvent.

Chromatography plates: after migration, lichen substances are developed by spraying with a 10% solution of sulphuric acid and heating the plates in an oven at 110°C.

Lichens exposed to sunlight.

The same lichens as the one on the left, but exposed to UV light, showing the presence of lichen substances absorbing the UV light. Molecules: the secret life of herbaria

A mysterious Madagascan plant: discovery of a new genus owing to DNA in herbaria

1963 A specimen with neither flowers nor fruit was collected in the Bermangidy forest of Madagascar. It came from an unknown tree in the Sapotaceae family (the family also of Shea butter and Argan oil). The specimen was archived in the herbarium of the National Museum of Na- tural History of Paris.

Late 1990s While working in the herbarium in Paris, we found the specimen, but were unable to connect it to any known species. The lack of flowers and fruits impeded even a determination to genus.

2009 At the CJBG we received a specimen with flowers for identification. It had been recently collected in the same Bemangidy forest of Madagascar. Surprise: it had the same leaves as the mysterious Madagascan plant in the herbarium in Paris. DNA analysis of the two specimens showed that they were genetically very close.

2010 The flowers of the new specimen resembled those of Tseb- ona macrantha, a beautiful tree found 500 km to the north, but with significant differences. To compare its DNA to that of the mysterious Madagascan plant, we went to Madagascar to get a sample.

2011 In November, we had opportunity to go to Bemangidy, and we collected further specimens of the mysterious Madagascan tree, and finally found the fruits, which were revealed to be quite different from those of Tsebona macrantha.

2012 DNA sequences confirmed that the specimens from the forest of Bemangidy, while related, was nonetheless rather distant from Tsebona macrantha. The mystery is now resolved: the new species doesn’t belong to the genus Tsebona, but rather to a new genus, previously unknown to botanists.

2013 In the journal Taxon, we published the description of the new genus, which we baptized Bemangidia, and the new species, Bemangidia lowryi. Molecules: the secret life of herbaria

The DNA of herbarium specimens is often fragmented due to poor drying con- ditions. Until recently, the information carried in these small fragments was scarcely usable. New high-output sequencing techniques however now allow reading millions of small-size fragments all at once. The entire genome can be reconstructed with the help of a complex set of computer programs. In this way, any herbarium specimen can potentially be sequenced. Since 2010, high-output sequencing of herbarium specimens has been rapidly expanding, and several projects are underway at the CJBG.

Traditional sequencing (above: a single DNA fragment is sequenced at a time) versus high output sequencing (below: millions of small fragments are sequenced at the same time, then assembled in order to reconstruct the whole genome). Herbaria lives – Species life

The herbarium specimen is the tangible proof of the existence of a given species at a particular place at a given moment. The herbarium is thus a dynamic archive which brings together information on the geographic distributions of species and their evolution over time. It therefore has a key role in the mana- gement of our plant and mycological heritage.

Mapping and predictions

Knowing the geographic coordinates of all the specimens for a species allows knowing the environments in which it appears and thus managing its conservation. In many tropical countries, collection efforts unfortunately have been poor. With the help of mathematical and statistical tools, it is now possible to predict, based on existing specimens, where a species has a good chance of being found. Such modeling similarly can predict the displacement of a species in response to climate change.

The known and potential distribution of Capurodendron greveanum (a tree of the Sapotaceae family) in Madagascar. The predicted distribution uses the geographic coordinates of various known collections for the species (red squares) together with environmental data to cal- culate the likelihood of encountering the species at any point of the territory (on the right). The closer the color is to orange, the higher the likelihood of encountering the species. Source: Garratt (2016) Herbaria lives – Species life

The herbarium as a tool in the struggle against invasive species

As an archive, the herbarium allows tracking the territorial advance of invasive species. Knowing the dynamics of expansion and the nature of the affected environments helps understand the behavior of the invading species and develop appropriate measures for its control or eradication.

Cotula coronopifolia, a plant in the sunflower family, is endemic to South Africa but was collected in sou- thewestern Corsica in 1954. It expanded rapidly, rea- ching the north of the island in 1990. It is now being considered for addition to an anticipated Black List of pernicious invasive species for Corsica. Source: Natali & Jeanmonod (1996), Candollea.

Horizontal Window The herbarium in the service of conservation

Our planet is currently under unusually intense pressure, and one out of five species is threatened with extinction. The estimation of the severity of this threat is based especially on earlier distributions inferred from herbarium specimens. Because of habitat destruction, many species can no longer be found in nature. Although a few of these are still cultivated in botanical gardens, most have disappeared forever.

Left Lysimachia minoricensis (of the primerose family), is a plant of the Balearic Islands of Spain, disappeared from its natural environment during the first half of the 20th century and is now only found in cultivation.

Right Casearia tinifolia (of the willow family), is an extinct species. All that remains of it is this one herbarium specimen, preserved in Geneva. Herbaria lives – Species life

Modern specimens and ancient distributions

The DNA of herbarium specimens allows calculating their degree of genetic similarity and constructing genealogies showing their evolutionary relationships and estimating times of diversification. When the geographic coordinates of specimens are taken into account, scenarios can be created for the colonization routes followed by the ancestors of our specimens, which spread generation after generation, ending up at their modern distributions.

Reconstitution of the life histrory of Silene gigantea (Carnation family) in Greece, Turkey, and the Aegean region

1.51-1.00 Mya 1.00-0.45 Mya 0.45-0.20 Mya 0.20-0.03 Mya

1.5 1.25 1.0 0.75 0.50 0.25 0 Millions of years ago (Mya)

Up Green zones represent the regions where populations of the species most likely were found at the time indicated in the upper left (Mya=millions of years ago). Yellow lines represent likely migrations routes.

Down Genealogical tree of the specimens. Source: Du Pasquier, Jeanmonod & Naciri (2017) Bot. J. Linn. Soc.