Spatial Analysis and Visualization of Genetic Biodiversity

Bacteria, viruses, and single-celled eukaryotes are vital components of the Earth’s biodiversity. Until recently, it has been nearly impossible to study these microorganisms outside of a laboratory setting due to their small size, immense population numbers, and enormous diversity. However, recent advances in DNA sequencing technology are opening up the microbial world for fine-scale examination. New ways of assessing microbial biodiversity and ecology have already produced stunning results: species counts in some habitats are thought to number in the tens of thousands, and microbial evolution appears to be driven in part by widespread sharing of genes among organisms. By comparing genetic data collected from many sample sites, we can investigate the interactions between the environment and microbial diversity, including the possible effects of spatial correlations among sites. Our ability to understand and learn from these data sets is limited by the availability of tools for analysis and visualization of sample sites, the distribution of microbial species and gene functions, and the evolutionary context of these organisms. We have developed GenGIS, a free and open source GIS package that provides tools for spatial visualization and analysis of microbial genome data. GenGIS renders maps in a three-dimensional OpenGL environment, and makes extensive use of other open-source software as well as publicly available geographic and genetic data. Here we describe the features of the first release version of our GIS, and use it to test questions about microbial biodiversity in the world’s oceans.