The art of phylogenetic inference

The art of using molecules to infer phylogenetic relations is to pick a molecule that evolves at a rate appropriate to the group of species in question. Different proteins, and stretches of DNA, evolve at different rates and can be used like clocks with hands that revolve at different rates. If you use a rapidly evolving molecule for an ancient group, the molecule will have 'turned over' many times during the phylogeny and once multiple changes at the same site become common the phylogenetic information in the sequence similarity is lost. Likewise, slowly evolving molecules are useless for fine phylogenetic resolution because they will not have changed enough.

Ribosomal RNA genes are particularly valuable in phylogenetic reconstruction because they are found in almost all species; they are present in both mitochondrial and nuclear DNA. The mitochondrial ribosomal RNA genes evolve more rapidly than the nuclear ribosomal RNA genes are useful for resolving phylogenetic problems in the 10 - 100 million year range whereas the slowly evolving nuclear ribosomal RNA genes are useful in the hundreds of millions of years range.