Development and Assessment of Bioinformatics Tools for Species Conservation and Habitat Management Melanie A. Sutton †‡ , Lori Deneke † , John Eme † , Wayne Bennett † , and Frank Wray † University of West Florida, Departments of Biology † and Computer Science ‡ Corresponding author: msutton@uwf.edu Abstract This project represents an interdisciplinary approach to integrating computational methods into the knowledge-discovery process associated with understanding biological systems impacted by the loss or destruction of sensitive habitats. We specifically developed bioinformatics tools for the study of (1) beach mouse communities and (2) marginal fish habitats. Data mining was used in these projects to intelligently query databases and to elucidate broad patterns that facilitate overall data interpretation. Visualization techniques that were developed present mined data in ways where context, perceptual cues, and spatial reasoning skills can be applied to uncover significant trends in behavioral patterns, habitat use, species diversity, and community composition. 1. Introduction Beach mice are small, nocturnal burrowing rodents that have a very specific habitat preference (see Fig. 1). They live only in primary and secondary sand dunes that populate barrier islands along the Gulf coast of Alabama and Florida, and on the Atlantic coast of Florida [1-3]. Fifty years ago, these habitats consisted of uninterrupted stretches of coastal dunes. Today, however, coastal exploitation has left suitable beach mouse habitat only in pockets of protected areas separated by miles of development. Similar situations have driven one subspecies of beach mice from Florida to extinction and others have been designated as endangered or threatened. Figure 1. Santa Rosa Beach Mouse dune habitats The marginal fish habitats of the Wakatobi Marine National Park in Sulawesi, Indonesia face similar threats of encroachment (see Fig. 2). Certain species of fishes found in these habitats complete their life cycle without entering the adjacent coral reef communities, whereas other species use the reef as a nursery for their young or as a foraging area [4]. Due to their proximity to shore and abundance of sea life, these sensitive areas are often the first to be disturbed by human activity, sometimes before the biodiversity and ecological relationships have been adequately surveyed [5-6]. Figure 2. Reef-associated marginal fish habitats Our goals in developing Internet-searchable databases and innovative multi-media-based visualization strategies for these two projects involve two objectives: (1) to streamline data analysis for these biological systems and (2) to provide virtual access as well as educational opportunities to these habitats for laypersons and students who might not otherwise be able to explore these areas. Tools developed for tracking the population dynamics of the Santa Rosa Beach Mouse will be used to study how habitat fragmentation impacts population dynamics, with the goal of facilitating the development of better management practices for related subspecies. Similarly, the implementation of a database for assessment studies of species diversity and community composition of sensitive marginal habitats is necessary for the establishment of practices to ensure diverse and productive reef and reef-associated systems. 2. Materials and Methods Researchers at UWF have tracked movement patterns of the Santa Rosa Beach Mouse monthly since July 2002 in the Gulf Islands National Seashore area of Santa Rosa Island in Florida. Mice are caught using live-traps that are baited with rolled oats. Upon capture, the animal’s mass, gender, relative age (adult or juvenile), and reproductive status are assessed. Mice are then released, with select animals marked using numerical ear tags. Proceedings of the Computational Systems Bioinformatics (CSB’03) 0-7695-2000-6/03 $17.00 © 2003 IEEE