From basepairs to birdsongs: phylogenetic data in the age of genomics

Given the quantity of molecular data now available, including complete genomes for some organisms, one can ask whether there is a need for any data beyond complete genomic sequences for phylogenetic analysis. One reason to look beyond the genome is that not all character information is encoded in organismal genomes. We propose a hierarchy of characters that ranges from biologically transmitted but nongenomically encoded characters, such as bird songs, to characters that are genomically encoded. All of these characters can retain historical information and are potentially useful for phylogenetic analysis. In addition, a number of phenotypic levels that are expressions of the genome can be identified. The question whether it is worth including any of these levels if all of the underlying sequence data have been collected arises, since issues of redundancy occur. Utilization of phenotypic levels that are ultimately based on sequences may facilitate reconstructing homologies that are not evident from sequence data alone. We propose the use of simultaneous analysis of sequence data and as many levels of phenotypic characters as possible to take advantage of homology information that may be more easily recovered from the latter. A method that eliminates redundancy to the degree that it can be detected is proposed.