Hello, I am a master student working on a research in bioinformatics, I have a problem understanding how biologists compare genomes for 2 species. what did they do with the polymorphism in the same specie ? for example when they say chimps genome are for 90% like the human genome ...and on the nucleotides level humans are a way different between themselves i.e blue eyes are coded with "ACGT" sequence wich is different than the brown eyes.
QuestionHow did scientist consider the polymorphism in the genome comparison and sometimes they say this taxa could be the ancestor of that ...
In a nutshell, polymorphisms within a species are not considered when doing cross-species comparisons because the polymorphisms may not be known (i.e. you have a single representative genome from each species) and because the frequency of change observed between two species is much higher than polymorphisms observed between two members of the same species. When you say that "humans are way different between themselves", they are less different between each other than either is to a chimp - thus why would the polymorphisms matter?
That's not to say it can't get slightly complicated. When biologists compare two genomes it's important to consider what is actually being compared, as different parts of the genome evolve at different rates (exons, introns, intergenic sequences, etc.), and for very closely related species at some loci I can see polymorphisms coming into play perhaps, but not in calculating overall distance. Perhaps you have a more specific question? Or an example of a quandary? Between pubmed and google you can find a wealth of information. See also: http://www.genome.gov/10001691 for a wealth of leads on genome comparisons.
