This is the era of whole-genome sequencing; DNA sequence data are becoming available at a rate unanticipated even a few years ago, providing biologists with both tremendous opportunities as well as serious challenges (because of the overwhelming mass of data). Comparative genomics is greatly aided by taking a phylogenetic approach: systematically relating nested sets of genomes on an evolutionary tree, using complex new computer algorithms. Natural history museums, and the research they enable, are thus poised to take an increasingly important role in collaborations with genomic biologists and computer scientists.

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.” 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 or the vertebrate backbone), by tracing the components back through simpler ancestral reconstructions, can lead to quicker understanding. Hence, phylogenomics allows one to go beyond the use of pairwise sequence similarities, and use phylogenetic comparative methods to confirm and/or to establish gene function and interactions. Most importantly for the systematist, the new comparative genomic data should also greatly increase the accuracy of reconstructions of the Tree of Life.

Berkeley Natural History Museums researchers are involved in an increasing number of genomics collaborations. Current projects include: