Twenty years ago, living microorganisms were named and classified on the basis of their morphology and physiology. This worked well for closely related taxa, but the higher level relationships between very distant lineages remained obscure because too few homologous characters were available for analysis. This situation changed dramatically in the 1980s following the invention of rapid and efficient methods for sequencing proteins and nucleic acids (both DNA and RNA). Suddenly, large numbers of homologous characters (single amino acids or single nucleotides) became available for comparison between closely and distantly related taxa. A concomitant development of computer-based methods for analyzing the new data (Section 9.2) has led to the production of “phylogenetic trees” which are designed to display, in a graphical way, the genealogical relationships between taxa at the tips of their branches. The same molecular methods have now been applied to representatives of most kinds of living organisms and they complement formal cladistic analyses based primarily upon shared-derived (synapomorphic) morphological characters.

These new methods have enabled a second approach to historical biology. The molecular comparisons may, in principle, produce information about the history of organisms with no fossil record. For example, colorful, tropical, soft-bodied molluscs known as nudibranchs are unknown as fossils. When did they first evolve? Molecular methods can provide an answer.

For Precambrian paleobiology the applications are obvious. However, the proportion of species with living descendants diminishes as one moves further backwards in time.