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Introduction to The Copenhagen databases of African vertebrates

The Copenhagen databases of African vertebrates

By Louis A. Hansen, Neil D. Burgess, Jon Fjeldså and Carsten Rahbek
Vertebrate species data presented on this web-site come from the one-degree resolution databases held at the Zoological Museum at the University of Copenhagen (ZMUC) in Denmark (version October 2006). These databases have been dynamic, and since first established in 1995 new data have been added almost daily; it thus represents the most complete cross-taxonomic database for any tropical continent developed so far. Data were compiled in the Worldmap Software (© Paul Williams, The Natural History Museum) in a grid of 1 x 1 geographical degrees, a resolution which we consider the best compromise between the sampling inadequacy for many species groups and the loss of biogeographic detail (especially in mountainous regions) at coarse resolutions. The data have been used for numerous research papers. Stacking the species maps on top of each other was used to obtain species richness estimations, which were then analyzed in relation to phylogenetic, environmental and social information, for objective and transparent analysis of the efficiency of conservation plans, or for development of objective biogeographical classifications. We are now making the revised and fully updated dataset available to the global community, for critical scrutiny and as a source for further research.
They are organized as four data files. These should be cited in the following way:
Galster, S., Burgess, N.D., Fjeldså, J., Hansen, L.A. and Rahbek, C., 2007. One degree resolution databases of the distribution of 1085 species of mammals in Sub-Saharan Africa. On-line data source-Version 1.00. Zoological Museum, University of Copenhagen, Denmark.
Hansen, L.A., Fjeldså, J., Burgess, N.D. and Rahbek, C. 2007. One degree resolution databases of the distribution of 1789 resident birds in Sub-Saharan Africa. On-line data source-Version 1.00. Zoological Museum, University of Copenhagen, Denmark.
Rasmussen, J.B., Hansen, L.A., Burgess, N.D., Fjeldså, J. and Rahbek, C., 2007. One degree resolution databases of the distribution of 467 species of snakes in Sub-Saharan Africa. On-line data source-Version 1.00. Zoological Museum, University of Copenhagen, Denmark.
Hansen, L.A., Burgess, N.D., Fjeldså, J. and Rahbek, C., 2007. One degree resolution databases of the distribution of 739 species of amphibians in Sub-Saharan Africa. On-line data source-Version 1.00. Zoological Museum, University of Copenhagen, Denmark.
The databases have been described in several papers (see especially Brooks et al. 2001). They have been extensively updated since then, as the species maps were updated and links to the sources data were established during 2000-2006. This work with updating the maps includes recent revision with 25 experts through visits to 12 museums in 8 countries. For the birds there are currently two databases which includes distribution maps for 1,975 species that have been refined over a period of 13 years using > 500 published papers, atlas studies (for 15 African countries), specimen data held at the Zoological Museum in Copenhagen (Denmark), and reliable internet data sources (for example the Tanzania bird atlas http://www.tanzaniabirdatlas.com). For mammals the current database includes distribution maps for 1,085 species that have been updated to follow the taxonomy of Wilson and Reeder (2005). Maps are based on data from >1,000 published papers and books, and recent updates includes visits during 2004-2005 to Smithsonian (Washington D.C.) and Field Museum of Natural History (Chicago). For amphibians the database includes maps of 739 species that have been based on data in >400 publications, including cross-checking with the online maps of the Global Amphibian Assessment (www.globalamphibians.org) and online taxonomy at Amphibian Species of the World (http://research.amnh.org/herpetology/amphibia/index.php). For snakes the database contains distribution records for 467 species that are based on more than 15 years work by the late Jens B. Rasmussen, including visits to more than 20 museums and referring to over 300 published papers (note, though, that ca. 200 strongly revised maps will not be made available on-line before JBR’s posthumous publications are in press).
A few words will be given here about the process of data compilation and rules used. The database covers the African mainland South of Sahara (20 degrees N); small offshore islands were excluded since island faunas evolve under other constraints as mainland faunas and are therefore not immediately comparable. Altogether 1,952 one-degree grid-cells are defined as representing the African mainland, but exactly which coastal cells that should be included depends on the map projection that is used. The distributional data comprise nearly 1 million within-grid-cell-records for 4,266 vertebrate species. The range maps represent historical distributions (ca. mid-20th century; plus actual distribution for megafauna), initially based on one or several published sources and later revised by one or several group experts. Range maps have gradually been refined by checking original data sources, a large number of recent site reports, as well as recently published national distribution atlases (for birds). This process has resulted in addition of “confirmed” records for many of the species. Range-maps assume a high degree of continuity between documented records, and especially for species which are common and have a high ability of dispersal a conservative interpolation is used, considering whether the intervening grid-cells comprise appropriate habitat (as assessed from habitat maps and satellite images, including Google Earth). However, the degree of interpolation depends on the expert judgment, and for species which are little known and generally considered rare, it is much less likely that we will extend the range into grid-cells between or adjacent to cells with confirmed records, based on the extent of the appropriate landscape formation. Negative records are also taken into account, for instance where a species is not recorded in a well-studied site with seemingly appropriate habitat, or if the area in question is occupied by a closely related (para)species. For poorly charted groups, such as most species of frogs and snakes, the mapped data are strictly limited to the confirmed record.
Because of the way in which the data were compiled over a long period of time, we are unable today to provide exact documentation for every in-grid-cell record. Instead, each species map in the on-line database is linked with a list of all references, which were used to generate that particular map.
A large number of people have assisted us with this project - for which we are very grateful. Foremost amongst these have been those who have helped to compile the species distribution and conservation status data across Africa, which forms the basis for all our work. We hope that everyone who has contributed is thanked below.
Museum collections consulted:
American Museum of Natural History – New York US, British Museum The Natural History Museum – London England, California Academy of Sciences – California US, Carnegie Museum of Natural History Pittsburgh US, County Museum of Natural History Los Angeles US, Durban Museum – Durban South Africa, East London Museum – East London South Africa, Royal Museum for Central Africa – Tervuren Belgium, Louisiana State University Museum of natural History – Louisiana US, Natural History Museum – Tring England, Natural History Museum – Paris France, South Africa Museum – Cape Town South Africa, The Academy of Natural Sciences – Philadelphia US, The Field Museum – Chicago US, Transvaal Museum - Pretoria South Africa, University of Dar es Salaam – Dar es Salaam Tanzania, University of Michigan Museum of Zoology – Michigan US, Western Foundation of Vertebrate Zoology – California US, Zoological Museum University of Copenhagen – Copenhagen Denmark. We also included data from many online databases, such as those of the National Museum of Namibia and African Biodiversity Information Centre of the Afrikamuseum, Tervuren.
We needed to find localities for numerous specimens in collection or those referred to in scientific paper. Some collecting sites are well-known, but for large numbers of others a careful scrutiny of published travel reports was needed, combined with modern gazetteers. Our main gazetteer source was NIMA GNS Public Page (http://gnswww.nga.mil/geonames/GNS/index.jsp), but we also used specific national gazetteers for a number of countries. Where specialists provided data, these may have used their own gazetteers to locate specimens geographically.
Species Distribution Maps
Birds: Taxonomy in general follows Sibley and Monroe 1990 and 1993, however where more recent literature strongly suggest a diverging from these, such is followed. New species described since the work of Sibley and Monroe (1990 and 1993) are added.
In 1993-95 Helen de Klerk compiled the initial distribution maps from the ‘Birds of Africa’ series of books, and for species not yet published (at that time) Hall and Moreau (1970) and Snow (1978) were used. There are two files, one with all species, including migrants and non-breeding occurrence of Africa’s resident species, and one with only the assumed breeding ranges within sub-Saharan Africa. The latter requires a qualified estimate of which records represent stragglers or migrations into areas where the species does not breed. These distribution maps were considerably checked and refined by a process of expert review, the addition of confirmed record data from all existing bird atlases for Africa, and from a thorough consultation and African bird literature. BirdLife International provided a copy of their Restricted Range Birds database (through M. Crosby and C. Bibby), and staff of the Percy FitzPatrick Institute in Cape Town, South Africa checked species distribution maps for southern African species. Other unpublished data were provided by N.D. Burgess, N. Cordeiro, J. Fjeldså, L.A. Hansen, J. Kiure, T. Lehmberg and D.C. Moyer (Eastern African Mountains), U. Gjøl Sørensen (ornithological visits to Africa), D. Pomeroy and H. Tushabe (Ugandan National Biodiversity Databank, Kampala), Forestry Department of Uganda (Biodiversity Survey Reports for Ugandan Forest Reserves), E. Waiyaki and L. Bennun (Reports of the Kenyan National Biodiversity Database), E. Baker and N. Baker (Tanzania Bird Atlas Project), P. Beresford and W. Jetz (Democratic Republic of Congo data), F. Dowsett-Lemaire and R. Dowsett (Congo/DRC Congo - 5N-5S, 10E-29E), and L. H. Holbech (Ghanaian forests). We also included data for the Albertine Rift area digitized by the African Biodiversity Information Centre of Afrikamuseum, Tervuren.
Mammals: Taxonomy in general follows Wilson and Reeder 1993 with updates from the 2005 version. Where appropriated, and with strong experts agreements or a publication suggest a different view such is followed.
Many of the distribution maps were compiled from the literature (see database). A number of people provided considerable assistance to the mapping work, namely: Shrews – R. Hutterer (Bonn, Germany) and P. Jenkins (The Natural History Museum, London); Bats- D. Kock (Senckenberg Museum, Frankfurt) and J. Fahr (Würzburg University, Germany); Elephant shrews – C. FitzGibbon (Large Mammal Research Unit, Cambridge) and G. Rathbun (US Fish and Wildlife Service), maps of confirmed localities of most larger African mammals: the late W.F.H. Ansell (Trendrine Press, St. Ives). Various other people assisted through providing references, unpublished information, or comments. These are as follows: G. Amori, S. Bearder, W. Bergmans, G. Bogliani, L. Boitani, G. Bronner, N. Burgess, C. Calessen, M. Carleton, W. Cotterill, G. Cowlishaw, J. Crawford-Cabral, G. Davies, M.J. Delany, F. Dieterlen, N. Dippenaar, R.J. Dowsett, M.B. Fenton, S. Galster, M.N.H.N. Gautun, M. Gimenez Dixon, N. Doggert, Frontier-Tanzania, S. Goodman, the late G. de Graaf, L. Granjon, P. Grubb, L.A. Hansen, M. Happold, D. Harrison, R.S. Hoffman, K. Howell, A.M. Hutson, D.C. Lees, H. Leirs, A.V. Linzey, W. Oliver, J. Patton, M. Perrin, P.A. Racey, L. Robbins, A. Rodgers, D. Schlitter, J.D. Skinner, S. Stuart, P.J. Taylor, N. Thomas, E. Topp-Jørgensen, R. Wirth, D.V. Van Cakenberghe, H. Van Rompaey, E. Van der Straeten, E. Vanden Berghe, the late W.N. Verheyen, V. Wilson, D. Yalden.
Snakes: Taxonomy in general follows a consensus made by the late Jens B. Rasmussen.
Many distribution maps used here come from the literature (see database), but every map was carefully scrutinized by the late J.B. Rasmussen of the Zoological Museum, University of Copenhagen. He also collected snakes in many parts of Africa (D.R. Congo, Sudan, Ethiopia, Tanzania) and in addition he revised the snake collections in his own institution and in the museums in Berlin, Bonn, Bruxelles, Chicago, Leiden, London, Oslo, Paris and Tervuren, literally taking (almost) every snake out of their jars to check their identities and label data. In this way he revealed a very large number of misidentified specimens, something that required quite dramatic changes of some species distributions compared to previously published maps. Several other people also provided data for various species or species groups of snakes mapped in this project: R. Botterweg, B. Branch, D. Broadley, B. Drewes, C. Gans, P. Gravlund, B. Groombridge, A. Jakobsen, K.M. Howell, B. Hughes, M. Lambert, D.C. Moyer, D. Meirte, O. Pauwels, L. Raw, S. Spawls, V. Wallach.
Amphibians: Taxonomy in general follows Frost 1985 and the online edition of 2004 and Duelleman 1993. New species described since the work of Frost 2004 and Duelleman 1993 are added.
Many of the maps of African amphibians are derived from the literature (see database), but others were updated or made using information provided by A. Schiøtz (African treefrogs), J. Poynton (African bufonids), A. Channing (southern African Amphibians), S. Loader (African Caecilians) and S. Stuart/IUCN-SSC (Red Data Book Amphibians). R. Botterweg, D. Broadley, N. Doggart, A. Duff-MacKay, B. Drewes, K.M. Howell, L. Raw and M-O. Rödel provided large number of other data.
Various staff and students have assisted with the mapping work over the 11 years of the vertebrate mapping project at the Zoological Museum, University of Copenhagen. Major inputs have been received from: S. Galster (mammal, amphibian and also bird data entering), LA. Hansen (all vertebrates, and general databases maintenance), J.B. Larsen (mammals), A. Jakobsen (amphibian data entering), L.L. Sørensen (mammals, amphibian data entering) and M.M. Westergaard (amphibian). The Zoological Museum has all the time supported the project with working space and making its resources available. Finally, K.T. Pedersen and C. Lange (DanBIF) formatted the data for the online presentation.
Financial support
N. Burgess, J. Fjeldså, L.A. Hansen and C. Rahbek received significant financial support for the vertebrate animals component of this project from the Danish Centre for Tropical Biodiversity, a ‘centre without walls’ in Denmark, financed by the Natural Science Research Council (grants 11-0390). This funding lasted from 1994 to 1999. Between 1999 and 2002 additional support for the development of the databases and for publishing scientific papers came from the Danish Council for Development Research and the Danish Natural Research Council (grants no. 980 2211, 21-00-0178 and 21-01-0547), the World Wide Fund for Nature-USA, The Newton Trust of Cambridge University in the UK, and from Conservation International of the USA. H. de Klerk was partly supported during her PhD studies by a grant from the Danish DANVIS Scheme for visiting scientists to Denmark. Visits to Copenhagen in August 2002 by N.D. Burgess and H. de Klerk were facilitated by grants from Copenhagen Biodiversity Centre (EU funding). Funding for finalizing the dataset for on-line access was provided by the Danish Council for Development Research (project 91173).
Neil Burgess worked for 5 years at the Zoological Museum of the University of Copenhagen in Denmark to facilitate the development of these databases, and the Zoological Museum is thanked for continuing to provide him access to the updated databases in order to complete this project. From 1999 to 2007 World Wildlife Fund (USA) allowed Neil Burgess to participate in the completion of this project and provided facilities to assist the work. The Zoological Museum, University of Copenhagen in Denmark, provided good working conditions for J. Fjeldså, C. Rahbek and L.A. Hansen. The Scientific Services Division of Western Cape Nature Conservation allowed H. de Klerk to participate in this project. Other institutions who provided their support were Conservation Science Group in the Zoology Department of the University of Cambridge, the Amphibians and Biogeography Sections in the Natural History Museum (London), the Botanical Museum of the University of Copenhagen (Denmark), the Environment Department at the University of York, CSIRO in Canberra Australia, the University of Dar es Salaam in Tanzania, and Makerere University in Uganda.
The Copenhagen databases of African vertebrates
Om samlingen af afrikanske vertebrater