Re: Can we distinguish species/subspecies from their genome maps?

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.