TreeBASE is a relational database designed to manage and explore information on phylogenetic relationships (Sanderson et al., 1993, 1994; Donoghue, 1994; Donoghue and Ackerly, 1996; Piel et al., 1996; Morel, 1996; Piel et al., 2000). Its main function is to store published phylogenetic trees and data matrices. It also includes bibliographic information on phylogenetic studies, and some details on taxa, characters, algorithms used, and analyses performed. The database is designed to allow retrieval and recombination of trees and data from different studies, and it can be explored interactively using trees included in the database. TreeBASE therefore provides a means of assessing and synthesizing phylogenetic knowledge.
Design and Content
TreeBASE was designed using ACI 4th Dimension database software and interfaces with WWW browsers using NetLink/4D. Click here (pdf version) to view our relational structure. The primary data objects in TreeBASE are bibliographic references to published phylogenetic studies, taxon by character data matrices, and phylogenetic trees resulting from the analysis of such data matrices. Information is also available that links data matrices and trees, including types of analyses performed, software used, etc. The TreeBASE web site allows searches to be performed in terms of taxonomic names or bibliographic keywords. Data matrices can also be downloaded from TreeBASE in nexus file format for further analysis (e.g., Sanderson and Donoghue, 1996).
Data are imported into TreeBASE using the nexus standard now used by several software packages for phylogenetic analysis (e.g., MacClade and Mesquite: Maddison and Maddison, 1992; PAUP: Swofford, 1993). However, we gladly accept other file formats (Hennig86, PHYLIP, etc.) and will simply translate them into nexus format for subsequent integration into TreeBASE. We have incorporated a mechanism to apply names to internal nodes in a tree, which facilitates browsing and expands query capabilities. Nexus files, including a data matrix and one or more trees, can also be downloaded for use in a wide variety of phylogenetic analysis programs.
Fig. 1. Relative proportion of vertebrate, invertebrate, plant, and fungal growth in TreeBASE. Here categories are stacked so that the relative contributions for each category can be compared. The height of the fungal line represents the sum of all categories.
For purposes of developing the initial prototype, we concentrated on assembling phylogenetic studies of green plants (especially angiosperms), fungi, and spiders. At present, however, most of our data comes from voluntary submissions and from journals that require or recommend that their authors submit to TreeBASE. TreeBASE is especially suited for phylogenetic and organismal journals -- in particular, it accepts more types of character data (e.g. RFLPs, morphological data, etc) than are accepted by other comparable databases (e.g. PopSet and EMBL-ALIGN). We hope that TreeBASE will continue to flourish as more journals and authors make use of it. Phylogenetic data can be easily and rapidly submitted to TreeBASE using several mechanisms, including as an enclosure in email, or, better yet, through our web submission forms.
Future Plans
Much of our effort in the near future will be devoted to populating the database with the results from more phylogenetic studies. This will entail various improvements in our submission forms and submission process. We also plan to expand the capabilities of TreeBASE in several ways. We hope to incorporate additional searching features. We are also working on algorithms for better visualizing the connectedness of "neighboring" trees, and for assembling partially overlapping trees into "supertrees."
In the near future we also plan to develop links to a variety of other databases and Internet resources. Some such links will be possible using the present system, but we anticipate the development of a new version of TreeBASE in a database system that will accommodate SQL queries and Internet activities. Interoperability will greatly expand the uses and capabilities of TreeBASE (see Blake et al., 1994). Thus, for example, linkage to databases of taxonomic names and classifications will broaden search capacities in TreeBASE by providing lists of synonymous names, included taxa, etc. Inclusion of accession numbers for molecular sequences (e.g., EMBL-ALIGN, EMBL-BANK, PopSet, GenBank) will allow links to additional information on these sequences, including information on the source of material and voucher specimens (e.g., SST). Linkage to the Maddison's Tree of Life web pages will provide ready access to images, descriptions, and additional references on the phylogeny of particular taxa of interest.
References
Blake, J. A., C. J. Bult, M. J. Donoghue, J. Humphries, and C. Fields. 1994. Interoperability of biological databases: a meeting report. Syst. Biol. 43:585-589.
Donoghue, M. J. 1994. Progress and prospects in reconstructing plant phylogeny. Ann. Missouri Bot. Gard. 81:405-418.
Donoghue, M. J. and D. D. Ackerly. 1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology. Phil. Trans. R. Soc. London B (in press).
Maddison, W. P. and D. R. Maddison. 1992. MacClade: Interactive Analysis of Phylogeny and Character Evolution, Vers. 3.0. Sunderland, MA: Sinauer Assoc.
Morell, V. 1996. TreeBASE: the roots of phylogeny. Science 273: 569.
Piel, W., M. Donoghue, T. Eriksson, C. Henze, K. Rice, and M. Sanderson. 1996. TreeBASE: a relational database of phylogenetic knowledge. Society of Systematic Biologists, St. Louis, Missouri (poster).<
Piel, W. H., M. Donoghue and M. J. Sanderson. 2000. TreeBASE: a database of phylogenetic information. Proceedings of the International Joint Workshop for Studies on Biodiversity, Tsukuba, Japan, in press.
Sanderson, M. J., B. G. Baldwin, G. Bharathan, C. S. Campbell, D. Ferguson, J. M. Porter, C. Von Dohlen, M. F. Wojciechowski & M. J. Donoghue. 1993. The growth of phylogenetic information and the need for a phylogenetic database. Syst. Biol. 42:562-568.
Sanderson, M. J. and M. J. Donoghue. 1996. The relationship between homoplasy and confidence in a phylogenetic tree. In press in Homoplasy and the Evolutionary Process (M. Sanderson and L. Hufford, eds.). San Diego: Academic Press.
Sanderson, M. J., M. J. Donoghue, W. Piel, and T. Eriksson. 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. Amer. Jour. Bot. 81(6):183.
Swofford, D. L. 1993. PAUP: Phylogenetic Analysis Using Parsimony, Vers. 3.1.1. Washington, DC: Smithsonian Institution.
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