Peter Stadler (University of Leipzig; SFI External Professor)
Abstract. The availability of complete genome-wide sequence information for large numbers of taxa provides new opportunities and poses new challenges for phylogenetic analysis. Implicitly, the genome sequence encode higher level features that in themselves contain phylogenetic information that can be analyzed independent of models of sequence information. Examples are repetitive elements, gene content and gene order, locations of introns, microRNA content, and RNA structures. Such features can serve as highly informative and relatively homoplasy-free characters, akin to morphological approaches. In order to make these features usable for large scale phylogenetic studies, however, one first has to extract them from the genomic sequence data.
While classical phylogenetics insists that "characters" are first identified and "homologized," phylogenomics also has to lead to use of "non-classical" characters, namely feature that are not defined or detectable with in a single genome and instead require an underlying genome-comparison for their identification. Examples include relative positional information in the form of synteny information or "near intron positions." Gaps in alignments are an even more extreme example.
In my presentation I will review some recent progress in this area, with an emphasis of deep metazoan phylogeny.