Vertebrate Mitochondrial DNA Phylogeny
Comparing data and methods for building phylogenetic trees using simple methods and readily available data. The mitochondrial genomes of vertebrates evolve at a rate roughly 10-fold faster than genes encoded on nuclear chromosomes. The Transitions and Transversions observed between pairs of sequences, vs their calculated phylogenetic distances, indicates that the mt-genomes have become saturated with mutations, and thus the distances to nodes deep in the tree (comparing mammals to reptiles or fish) are significantly underestimated. These trees would indicate that mammals diverged from other tetrapods very soon after then tetrapods diverged from fish. But the fossile record, and phylogenies from nuclear chromosomal DNA and other data, all agree that there was considerable time elapsed between tetropods splitting from fish and the earliest mammals. The point of these analyses of the data is to illustrate how saturation with mutations can distort phylogentic reconstructions to some degree.
Different programs can treat data with saturation of silent sites differently. The largest difference I have observed so far, is using the IQTree program which expands the distance between the nodes deep in the tree.