Browsing by Subject "Biodiversity informatics"
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Item The fluviageny, a method for analyzing temporal river fragmentation using phylogenetics(2015-05) Gordon, Andrew Lloyd; Howison, James; Arctur, David KPhylogenetic trees have historically been used to determine evolutionary relatedness between organisms. In the past few decades, as we've developed increasingly powerful computational algorithms and toolsets for performing analyses using phylogenetic methods, the use of these trees has expanded into other areas, including biodiversity informatics and geoinformatics. This report proposes using phylogenetic methods to create "fluviagenies" - trees that represent the effects of river fragmentation over time caused by damming. Faculty at the Center for Research in Water Resources at the University of Texas worked to develop tools and documentation for automating the creation of river segment codes (a.k.a., "fluvcodes") based on spatiotemporal data. Python was used to generate fluviageny trees from lists of these codes. The resulting trees can be exported into the appropriate data format for use with various phylogenetics programs. The Fishes of Texas Database (fshesoftexas.org), a comprehensive geospatial database of Texas fish occurrences aggregated and normalized from 42 museum collections around the world, was employed to create an example of how this tool might be used to analyze and hypothesize changes in fish populations as a consequence of river fragmentation. Additionally, this paper serves to theorize and analyze past and future potential uses for phylogenetic trees in various other fields of informatics.Item The use of modern digital technology to store and serve biodiversity data for research and educational purposes(2015-12) Brenskelle, Laura Marie; Rowe, Timothy, 1953-; Bell, Christopher J; Brown, Matthew; Karadkar, UnmilHerein I describe two different projects I completed during the course of my Master’s at The University of Texas at Austin. These projects broadly focused on the application of technology to maintain scientific data for research and education. The first chapter is a case study of a website I developed as part of a group project in a graduate database management course. Our group took a module from proprietary instructional software developed in the 1990s, and moved it into an online format with a MySQL database on the backend. In chapter one, I provide the appropriate documentation for this project to be expanded in the future. The second chapter describes a project where I interviewed collection managers of natural history collections about their database practices. These practices have implications for the downstream use of these data for research, education, and conservation. As technology inevitably advances, this thesis will serve as a historical snapshot of modern practices, and today, it can provide a starting point of how to further the emerging discipline of biodiversity informatics.