Early work used the proteins which are produced by gene action, but recent work has concentrated on DNA, the genes themselves.
Ribosomal DNA (rDNA)
The genes coding for the RNA of ribosomes (rRNA), most often the small subunit 18SrRNA, are used (the gene is called 18SrDNA). This gene is very highly conserved, i.e. has changed very slowly in evolution, no doubt because it has an important structural role and mutations are unlikely to survive natural selection. It can therefore provide evidence about changes that occurred very early in animal evolution, such as the separation of classes within a phylum or even the origin of new phyla.
Genes regulating early development
Hiese may be very informative, as genes acting early in development order the fate of whole blocks of cells. Comparisons between phyla are therefore based on molecular evidence quite different from that obtained using ribosomal genes, where information is obtained about the amount of sequence divergence that has occurred over evolutionary time. Using more than one gene and testing different aspects of evolutionary change may avoid some of the disadvantages inherent in using ribosomal genes alone.
Mitochondrial DNA (mtDNA)
Hie genes situated in the mitochondria, outside the nucleus and different from the nuclear genes, are useful sources of information. In most animals the sperm contributes no material to the zygote, and therefore mitochondrial inheritance is confined to the female line: the use of mtDNA is simplified by its uniparental origin. Mitochondrial DNA changes relatively fast in evolution and is useful at the short end of the evolutionary time scale, to resolve changes that occurred less than 15 million years ago such as the separation of genera and species. When the whole (small) genome can be sequenced, mtDNA can also tell us about ancient changes. More often, it is not the gene content of the mitochondria that is used but the order of genes round the chromosomal ring.