"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200B Spring 2011

This is the era of whole-genome sequencing; molecular data are becoming available at a rate unanticipated even a few years ago. Sequencing projects in a number of countries have produced a growing number of fully sequenced genomes, providing computational biologists with tremendous opportunities. However, comparative genomics has so far largely been restricted to pair-wise comparisons of genomes. The importance of taking a phylogenetic approach to systematically relating larger sets of genomes has only recently been realized. A recent synthesis of phylogenetic systematics and molecular biology/genomics – two fields once estranged – is beginning to form a new field that could be called "phylogenomics" (Eisen 1998). Something can be learned about the function of genes by examining them in one organism. However, a much richer array of tools is available using a phylogenetic approach. Close sister-group comparisons between lineages differing in a critical phenotype (e.g., desiccation or freeze tolerance) can allow a quick narrowing of the search for genetic causes. Dissecting a complicated, evolutionarily advanced genotype/phenotype complex (e.g., development of the angiosperm flower), by tracing the components back through simpler ancestral reconstructions, can lead to quicker understanding. Hence, phylogenomics allows on