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Millions of plants online

Virtual herbaria—compilations of information on plant collections maintained in other countries—facilitate analysis of Brazilian biodiversity

Branch of a sweet potato plant collected in Anavilhanas, Amazonia, in 1991: preserved at the New York Botanical Garden

New York Botanical Garden / RefloraBranch of a sweet potato plant collected in Anavilhanas, Amazonia, in 1991: preserved at the New York Botanical GardenNew York Botanical Garden / Reflora

During two trips planned for 2015, Sergio Romaniuc Neto of the Botanical Institute of São Paulo intends to retrace the plant-collecting expeditions undertaken by French naturalist Auguste de Saint-Hilaire in 1819 and 1822 along the coast between São Paulo and Rio de Janeiro and through inland São Paulo State. Romaniuc Neto knows precisely which plants to look for because, in addition to having seen the specimens preserved at the National Museum of Natural History in Paris, he was one of the coordinators who put together the online version of Saint-Hilaire’s collection of plants and field notebooks (, which has been in operation since 2009. As they expand in Brazil, these so-called virtual herbaria bring together information and millions of detailed images of collections of Brazilian plants, organized by botanists in Brazil or elsewhere, that were previously kept only in cabinets at their institutions. This online collection aids researchers in their work, expands the number of users and enables researchers to perform new types of analysis of Brazil’s biological diversity—all of which would have been inconceivable just a few years ago.

“Before, we had to take long trips to see the collections in other countries, without knowing what we might find,” says Rafaela Forzza, a researcher at the Rio de Janeiro Botanical Garden. “Now, with virtual herbaria, we can more effectively plan and choose what we want to study before traveling.” Forzza coordinates Reflora (, a program that repatriates information on Brazilian plants, launched in 2010 with support from the Brazilian federal government, research foundations and businesses. Reflora has made publicly available online some 100,000 images of Brazilian plants at the Kew Botanic Gardens near London, and another 75,000 images from the National Museum of Natural History in Paris.

The two institutions sent images of the plants, and the team at the Botanical Garden analyzed the labels of each specimen, which are written in French, English, German or Latin, to obtain metadata on the name of the collector, date and location of collection, and other details to complete the identification. Forzza says that each day, her team of 70 grant recipients and staff members working at several institutions capture, examine and process information on about 750 images that arrive from herbaria in other countries, and another 750 from the Botanical Garden’s own virtual herbarium. “It’s now routine practice: no plant goes into the herbarium’s physical collection without first being photographed and incorporated into the online collection,” she says.

Through agreements established in late 2014, herbaria in other countries have begun to send images of Brazilian plants in their collections. The New York Botanical Garden has sent 52,000 of its planned 320,000 images. The University of Missouri Botanic Garden has sent 17,000 of an estimated total of 170,000 images. Soon, thousands of images will also begin to come in from museums in Vienna and Stockholm. These images will help researchers to distinguish the earliest records, known as type species, which are of key importance in knowing whether the assumedly new plants they have collected are in fact new. The type species of cassava (Manihot esculenta), for example, collected in 1850 in Santarém, state of Pará, is kept in the Paris herbarium, but it can be viewed in detail using Reflora.

The first botanical record of cassava: specimen collected in 1850 in the city of Santarém and kept at the Paris-based herbarium

New York Botanical Garden / RefloraThe first botanical record of cassava: specimen collected in 1850 in the city of Santarém and kept at the Paris-based herbariumNew York Botanical Garden / Reflora

Since 2014, Reflora has been adding to the digitized collection of plants kept in 11 herbaria at universities, museums and research centers in the states of Bahia, Sergipe, Rio Grande do Norte, Ceará, Minas Gerais, Espírito Santo, São Paulo, Paraná, Santa Catarina, Rio Grande do Sul and the Federal District,. “Virtual herbaria do not reduce the need for, or the space devoted to, the physical collections, but they provide a means for safeguarding the materials, and they are an aid to consultation and strategy-making for conserving Brazilian flora,” Forzza notes. The information in virtual herbaria should prove useful for the preparation of a detailed document about the status of the 45,941 Brazilian plant species, which is to be completed by 2020 as stipulated in the Convention on Biological Diversity, an international treaty to which Brazil is a signatory.

The Reference Center on Environmental Information (CRIA), in the city of Campinas, is responsible for developing and maintaining the speciesLink network, another database of Brazilian biodiversity. SpeciesLink ( shares over 7.2 million records on 103,000 species of animals, fossils, microorganisms, plants and fungi in the physical collections of 123 institutions in every state in Brazil, as well as 11 research centers in other countries. The speciesLink network is the database of the National Institute of Science and Technology (INCT) – Virtual Herbarium of Flora and Fungi (, an assemblage of 152 collections, 5 million records and 900,000 images of 77,500 different species. “Each herbarium sends its open data information,” says Dora Canhos, associate director of CRIA. “Now, not only the large herbaria, but also the small ones far from metropolitan areas, are being digitized and have an opportunity to make their collections available to the community.”

The team at CRIA gained its first experience in this area in 2000 when they developed SinBiota, a system designed to consolidate and manage information from surveys of plants, animals and microorganisms conducted by researchers in São Paulo State connected with the Biota-FAPESP Program. SpeciesLink took root soon afterward, providing information on the biodiversity of São Paulo State, and eventually that of other states as well. In 2006, CRIA launched the electronic version of Flora Brasiliensis (—with descriptions of 22,767 species in 15 volumes produced between 1840 and 1906—and began collaborating with institutions in other countries, in particular the botanical gardens of New York and Missouri, to repatriate information on plants collected in Brazil.

Strawflower (Comanthera nivea): at Kew since 1887, reviewed by USP botanists in 1993 and by Reflora in 2011.

New York Botanical Garden / RefloraStrawflower (Comanthera nivea): at Kew since 1887, reviewed by USP botanists in 1993 and by Reflora in 2011.New York Botanical Garden / Reflora

One of the most recent projects was the production of the Saint-Hilaire Virtual Herbarium, which contains 9,000 records and about 4,500 type species. In 1816, shortly after arriving in Brazil, the French naturalist was the first to describe erva mate (Ilex paraguariensis) found on a farm near the city of Curitiba in the state of Paraná, and the pequi tree (Caryocar brasiliense), found in Minas Gerais. By the time he returned to Europe in 1822, he had also traveled around the states of Rio de Janeiro, Goiás, São Paulo, Santa Catarina and Rio Grande do Sul, as well as parts of Argentina and Paraguay. His 10 field notebooks, now included in the virtual herbarium along with descriptions of his collected specimens, contain comments about the local customs of the places he visited. For that reason, says Canhos, “it is a tool for historians and sociologists alike.”

These accounts were published in books that offer vivid portraits of the landscape, such as that found in Segunda viagem a São Paulo e quadro histórico da província de São Paulo [Second voyage to São Paulo and historical overview of the province of São Paulo]. “Above all, I admired the brightly illuminated Carmo church,” he wrote upon arriving in São Paulo in 1822. “The streets were filled with people strolling from one church to another, but only to have a look at them, without the slightest hint of devotion. Women selling confections and sweets sat on the ground, in the doorways of churches, and villagers bought the delicacies to offer to their female strolling companions.”

Romaniuc Neto perused Saint-Hilaire’s notebooks during his doctoral studies at the Museum of Natural History in Paris between 1996 and 1999. After returning to São Paulo, he undertook a project to digitize the plants and field notebooks and, with support from FAPESP and the Vitae Foundation, formalized the cooperation agreement between the Paris-based museum, the Botanical Institute and CRIA. He then returned to Paris to search for the plants collected by Saint-Hilaire, which were scattered throughout the collection of 12 million specimens, in his effort to produce the virtual herbarium.

He now plans to use this information in spatial and historical analyses. “Are we really losing biodiversity? How, and how much? Might other species have emerged in the same space as the earlier ones, and thereby maintain the diversity? Should we protect spaces, or species? Only historical and spatial analyses of the biodiversity can help us answer these questions,” he says. Rafaela Forzza, of the Rio de Janeiro Botanical Garden, adds, “In order to move forward, we need the past.” The botanists are satisfied to see one of their long-time dreams—online herbaria—take shape, but they are also concerned that the difficulty of obtaining long-term funding could jeopardize the continuity of these databases of Brazilian plants.

Saint-Hilaire Virtual Herbarium (No. 2006/57363-4); Grant mechanism Regular Line of Research Project Award; Principal investigator Sergio Romaniuc Neto (Botanical Institute-SP); Investment R$60,123.56 (FAPESP).

Scientific article
PIGNAL, M. et al. Saint-Hilaire virtual herbarium, a new upgradeable tool to study Brazilian botany. Adansonia. V. 35, No. 1, p. 7-18. 2013.