Q3. If we compare genome and found 5% differences between them, does this mean that the two organisms are really different from each other?
The percentage difference is not necessarily the best indicator of divergence between species. The genomes consist of different elements, some of them more important for the organism than the others. For example, genes change very little, since they are restricted by their function. On the other hand, the intergenic (between genes) sequence and introns often change a lot, because it has no protein coding purpose. Still the differences can be very deceiving. For example, humans and chimpanzees are 5% different. This seems like definitely a lot of difference. However, these differences are not found in genes, and it is not clear which ones of them make us human. On the other hand, two sea urchins born from the same individual, are often almost 4% apart, almost as much as humans and chimpanzees. This may seem surprising, but there is an objective explanation: there is a lot of variation inside the same species. A lot of this is explained by the adaptation to the changing environments, most of the differences are found in the immune genes.
http://www.nsf.gov/news/news_summ.jsp?cntn_id=108174
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