| Motivation. Large scale sequencing of the 16S ribosomal RNA (rRNA) gene from microbial populations has lead to the deposition of thousands of environmental clone sequences in GenBank. Because only a small fraction of microorganisms will grow in pure culture, the sole information about the biology of much of life's diversity is the environmental distribution of these sequences.; UniFrac. In order to compare diverse microbial communities and to determine the degree to which different physical and chemical factors, such as temperature, nutrient concentration, or geographical location, impact microbial composition, I developed a new diversity measure called UniFrac. UniFrac calculates phylogenetic distance between communities as the fraction of branch length that leads to descendants of one community or the other but not both. I also developed weighted UniFrac, which additionally accounts for relative sequence abundances, and show that applying weighted and unweighted UniFrac to the same data provides different but equally illuminating insights into the important factors for explaining microbial distribution. To make UniFrac and related phylogenetic diversity measures available to the community of microbial ecologists, I helped to develop a web implementation, which is available at http://bmf.colorado.edu/unifrac.; Global analysis. I performed the most comprehensive analysis of the environmental distribution of bacteria to date, based on 21,752 16S ribosomal RNA (rRNA) sequences compiled from 111 studies of diverse physical environments. I used UniFrac to cluster the samples based on similarities in the phylogenetic lineages that they contain, and found that, surprisingly, the major environmental determinant of microbial community composition is salinity, rather than extremes of temperature, pH, or other physical and chemical factors represented in the samples. I also used these clusters to group the samples into environment types and determined which environment types are the most phylogenetically diverse. Sediments were more diverse than any other environment type. Surprisingly, soil, which has high specieslevel diversity, has below-average phylogenetic diversity. This work provides a framework for understanding the impact of environmental factors on bacterial evolution, and for the direction of future sequencing efforts to discover new lineages. |
