Before the era of molecular biology, species were organised based on their physical characteristics.
This, however, has turned out to be somewhat incorrect, as many lineages converge to the same outcome after initially being separated. For example, there are different species of flying squirrel which live on different continents. Their last common ancestor was not a flying squirrel, and following separation onto different parts of the world, they continued evolving separately.
Due to similar niches in their environment, they happen to have both evolved their flying ability further down the line. This is called convergent evolution and it led scientists to assume these species must be closely related since they look similar. Similarly, archaea used to be lumped in with bacteria due to their apparent similarities, only to later be found to be separate altogether.
Molecular biology techniques such as genetic fingerprinting have enabled researchers to compare organisms and species on an unprecedented level with much more data and detail, to be able to ascertain their…