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A New Era for Specimen Databases and Biodiversity Information Management in South Africa

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A New Era for Specimen Databases and Biodiversity Information Management in South Africa Biodiversity Informatics, 8, 2012, pp.1-11. A NEW ERA FOR SPECIMEN DATABASES AND BIODIVERSITY INFORMATION MANAGEMENT IN SOUTH AFRICA WILLEM COETZER, OFER GON South African Institute for Aquatic Biodiversity, Somerset Street, Grahamstown, South Africa. Email for correspondence: [email protected]. MICHELLE HAMER South African National Biodiversity Institute, Cussonia Ave, Pretoria, South Africa FATIMA PARKER-ALLIE South African National Biodiversity Institute, Rhodes Drive, Cape Town, South Africa Abstract. ‒ We present observations and a commentary on the inherited legacy and current state of biodiversity information management in South African natural history museums, and make recommendations for the future. We emphasize the importance of using a recognized database application, and training and capacity development to improve the quality and integration of biodiversity information for research. In the last decade, biodiversity information in approximately 26% (Hamer 2011) of vouchered specimen databases of natural history museums specimens in South African zoological collections has seen renewed interest and much innovation could be queried through the SABIF Data Portal and development (Bisby 2000, Soberón and or the GBIF Data Portal. Peterson 2004, Johnson 2007, Peterson et al. The vast majority of information about South 2010). Biodiversity Informatics has been defined African biodiversity, which is relatively well as ‘application of informatics to recorded and yet- sampled (Figure 1), originates from South African to-be discovered information specifically about natural history museums and the South African biodiversity, and the linking of this information Bird Atlas Project (Table 1). with genomic, geospatial and other biological and Biodiversity information, including specimen non-biological datasets.’ The mission of the records from natural history collections, is used Global Biodiversity Information Facility (GBIF1) in: is to ‘facilitate free and open access to • Biodiversity monitoring (e.g., Reyers and biodiversity data worldwide via the Internet to McGeoch 2007); underpin sustainable development.’ As of January • Bioregional planning (e.g., Smith and 2012 the GBIF data portal provided access to Wolfson 2004); >317 million primary biodiversity data records. • Identifying and categorizing threatened By January 2011 ~7.1 million records on the species (e.g., Tweddle et al. 2009); GBIF data portal were contributed by the South • Understanding the impacts of global change African Biodiversity Information Facility on biodiversity (e.g., Skelton and Coetzer (SABIF), to which natural history museums in 2011, Cherry 2009, Skelton et al. 1995) and South Africa contribute their biodiversity developing mitigation strategies; information. These records originated from 8 • Informing sustainable harvesting programs; South African data providers (mostly natural • Control of alien, invasive species (e.g., history museums) and 14 collections. Eighty per Foxcroft et al. 2009) and disease vectors; cent of the records were unvouchered occurrences, • Environmental impact assessments. mostly observation records from the South African Bird Atlas Project, contributed by the Ecological niche modeling (Phillips et al. Animal Demography Unit of the University of 2006) is a productive research area that relies Cape Town. In January 2011 the digital records of heavily on high-quality biodiversity data, especially with respect to taxonomic precision and 1http://www.gbif.org/. precision of georeferencing. Maintaining such 1 Biodiversity Informatics, 8, 2012, pp.1-11. high-quality data requires a well-designed and well-managed relational database and application, tailor-made for biodiversity information. Perhaps the most practical use of biodiversity information is in systematic conservation planning, to identify areas that need to be protected for the persistence and spatial continuity of genetic variability (populations), species, communities or ecological services (Nel et al. 2011). The biodiversity community has recently drawn extensively on biodiversity information held by South Africa’s natural history museums for important, national Figure 1. The density of occurrences of South African biodiversity projects. Examples of these are the biodiversity as published by GBIF Alien Zonation Project (NEM:BA, 2004), the in April 2012. National Freshwater Protected Areas Project (Nel et al. 2011) and the National Spatial Biodiversity Assessment (Reyers et al. 2007). Table 1. Numbers of specimen occurrences of South African biodiversity contributed to GBIF as of April 2012. Numbers in parentheses refer to vouchered specimens. Country Georeferenced occurrences Georeferenced as % of total Not georeferenced Argentina 14 <0.05 0 Australia 3,676 <0.05 2,395 Austria 775 <0.05 4,352 Belgium 4,003 <0.05 3,406 Canada 1,501 <0.05 1,019 Colombia 15 <0.05 0 Denmark 1,284 <0.05 319 Estonia 6 <0.05 139 Finland 733 <0.05 1,179 France 612 <0.05 24,754 Germany 35,604 0.05 21,403 Hong Kong 2 <0.05 0 India 236 <0.05 0 Japan 6 <0.05 1,556 Mexico 56 <0.05 176 Netherlands 2,056 <0.05 6,201 New Zealand 0 <0.05 105 Norway 376 <0.05 0 Poland 529 <0.05 764 Portugal 0 <0.05 38 South Africa 7,115,071 (2,295,813) 98.3 (94.8) 638,843 Spain 132 <0.05 531 Sweden 1,643 <0.05 36,594 Switzerland 2 <0.05 16,014 Taiwan 1 <0.05 0 United Kingdom 2,166 <0.05 37,773 United States 69,496 1 71,476 TOTAL 7,239,995 (2,420,737) - 869,037 As the ultimate, verifiable source of much preservation and management of collections of biodiversity information, natural history museums physical specimens, but also for capturing, are now not only responsible for the curation, managing and disseminating accurate, precise, 2 Biodiversity Informatics, 8, 2012, pp.1-11. and current biodiversity information in the form COORDINATED BIODIVERSITY INFORMATION of up-to-date species names and specimen records. MANAGEMENT IN SOUTH AFRICA Similarly the perception of a specimen database is Drinkrow et al. (1994) were among the first to changing from that of a pure collection highlight the need for greater recognition of the management tool to include the concept of a value of South African natural history collections ‘biodiversity specimen database’: a repository of in biodiversity research, specifically the need for useful research data relating to occurrences of coordinated biodiversity database management biological species in spatial, environmental and through a national biodiversity network. In the temporal contexts. As the former, the database is late 1990s, such an initiative was launched. used independently of other organizations’ Named BioMAP (and later renamed SA-ISIS), it specimen databases, in an inward-looking fashion was the first coordinated program to capture, (e.g., Coetzer et al. 2009), but as the latter, the collate and disseminate South African information from different databases and biodiversity information, including specimen organizations needs to be integrated in records from natural history collections. interoperable systems, to discover and analyze SABIF was established as a program under the patterns in biodiversity, and to detect changes in management of the National Research Foundation these patterns, including those caused by global (NRF) in 2003, following the signing of a change. In this article we consider some of the Memorandum of Understanding with GBIF. In challenges faced by the South African 2006, SABIF was incorporated into the South biodiversity community with respect to African National Biodiversity Institute (SANBI). biodiversity information management, and As a node of GBIF, the objectives of SABIF are emphasize the importance of adopting a more similar to those of GBIF: to mobilize biodiversity systematic and rigorous approach to formal data, provide a data-sharing platform, promote biodiversity information management in South data standards and tools, and develop capacity in, African natural history museums. and raise awareness of, biodiversity informatics. We believe that training and skills- Progress in digitizing South African natural development will be central to any strategy that history collections can be traced back almost two seeks to improve biodiversity information decades (Gon and Wertlen 1996), but the recent management in South Africa. In the last decade, development of information technology has far we have witnessed the development of a outpaced the development of skills in museums. staggering array of standards, recommendations, South African custodians of natural history products, tools, initiatives, and collaborations collections have been unable to address this focusing on biodiversity informatics. We should disparity, particularly in the present context of not postpone introducing young technical staff underfunded and understaffed natural history into this new world any longer. museums (Cherry 2009). This situation contrasts Information management is not the only with the recognition of South Africa as a challenge faced by natural history collections in megadiverse country with a tradition of South Africa. In 2010, a survey of zoological excellence in collection management and research collections was undertaken to assess the state and in biodiversity science. In the last five years, sustainability of collections. The report however, a user-community of people directly representing the initial outcome of the survey involved in biodiversity informatics has been (Hamer 2011) found that collections could be formed under the auspices of SANBI to address
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