A phylogeny is a statement about the evolutionary history of organisms. Cladograms give branching order only, but phylograms include branch lengths as well. They inform us about diversification of lineages, patterns and rates of trait evolution, and the ages of taxa and timing of radiations.
The tree is a model for the history of life at the macroevolutionary level. Darwin fully embraced the idea.Trees now being built with DNA sequence data, using improved phylogenetic algorithms and increased computational power. We now have many well-supported phylogenies backed up by multiple lines of evidence.
There are issues with correlating gene trees with species trees — there can be discordance because of coalescence, etc.
There is some controversy about how much lateral gene transfer confounds the tree model of evolution. Are there parts where the tree model breaks down completely? Some microbiologists argue that archaeobacteria and prokaryote phylogeny can’t be fit into a tree; the sensationalist New Scientist cover was shown. Ward thinks it is an exaggeration. Lateral gene transfer occurs, but Wu and Eisen analyzed 31 conserved protein coding genes in archaea and bacteria and a well-resolved phylogeny still emerges. This argues that lateral gene transfer was not so rampant that it obscures the central tree.
Ward showed a diagram from the Creation “Museum”, illustrating their belief in an “orchard of life”. They need to do a pseudo-phylogenetic analysis to show the “kinds” of life; much of their language has been taken from phylogenetic systematics. He calls it a cargo cult science.
What do the new molecular phylogenies tell us about evolution. Convergence is widespread; morphology can mislead us about evolutionary history. We’re seeing well-supported clades emerging, such as the afrotheria, scattered within old morphological trees. We’re also seeing a stronger biogeographic pattern in the data.
We also have tools for reconstructing ancestral states: we’re using molecular/genetic data to infer and reconstruct an ancestral form. We can use this to reconstruct ancestral protein sequences, which can then be synthesized and their biological properties measured. Ward described the work of the Thornton lab on reconstructing glucocorticoid receptors.
Phylogenies also provide new insight into concepts of higher, more inclusive taxa. Specific example is the persistence of the dinosaur clade beyond the K/T boundary in the form of birds.
Non-pc taxon names: just as the fish taxon excludes tetrapods, inscts seem to be modified crustaceans, butterflies are modified moths, ants are modified wasps.