To Tree or Not To Tree: Phylogeny and Microbial Community Comparisons
Rob Knight, HHMI and Department of Chemistry & Biochemistry, University of Colorado at Boulder
Monday, November 30, 2009
4:00 p.m., 223 Weber
The explosion of 16S rRNA sequence data in the public databases and the availability of high-throughput sequencing methods enables us to get a global view of microbial diversity for the first time. One key issue is how we should compare communities: should we use a similarity cutoff and treat all taxa at that level equally, as is commonly done for macroorganisms, or should we use information about the relationships among taxa? Similarly, should we focus on presence/absence of specific lineages, or on measures that take abundance into account? In this seminar, I describe some of the advantages and disadvantages of using the phylogenetic approach, as in our UniFrac software, and show the implications of the different approaches for the clustering of samples from hundreds of diverse environments, including a range of free-living and animal-associated environments. I argue that even a very bad tree is more useful for community comparisons than the star phylogeny that tree-independent methods implicitly assume.