|MadSci Network: Genetics|
For two unknown organisms this would be extremely difficult. The main difficulty arises from the distribution of variability within and between species. In order to use genetic variability to differentiate taxonomic groups one would need to know what specific sites are diagnostic for the groups. These sites would have to be different between the groups while being invariant within the groups. Because each individual's genome is quite variable with respect to another individual of the same species/subspecies (depending where in the genome you look) it is possible that the variation seen at certain sites could be shared across taxonomic groups just by chance. The 2% similarity between chimpanzees and humans (and this is for one species of chimpanzee. The bonobo wasn't part of this analysis) derives from a very "crude" genomic comparison based on how disassociated DNA molecules from the two groups cross-hybridize (form a double-stranded molecule with one strand from each species). Unfortunately there doesn't appear to be a strict numerical relationship that one can use to relate levels of similarity/difference and membership in taxonomic groups, even though many have tried to find one. The level of variation seen within one taxonomic group can be equal to or greater than that measured between groups, especially if the groups have been separated for a long period of time. Long periods if independence allow variability within groups to accumulate. As the genome is not infinite, and because variability is not uniformly distributed across the genome, groups that have been separated for long periods of time can, by chance, have similarities that would group them together rather than separate them. This is known as homoplasy and is one of the major stumbling blocks on molecular systematics.
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