Hey Asaf, I will try to assist you.
1. Penny et al examined protein sequences in a group of 11 species. They used the pattern of amino acid similarities to work out the "tree" for the specieis. Some species have more similar protein sequences than others, and the more similar species are grouped more closely in the tree. The observation that suggests evolution is as follows. We start by working out the tree for one protein. We can then work it out for another protein and compare the trees. Penny
et al worked out the tree for the 11 species using each of the five proteins. The key observations was that the trees for all five proteins are very similar. For 11 species, there are 34,459,425 possible trees, but the five proteins suggests trees that form a small subclass from this large number of possible trees. The similarities and differences in the amino acid sequences of the five proteins are correlated. If two species have more amino acid homologies for one of the proteins, they are more likely to form the other proteins.
coalescent tree charts the ancestral relationships for a set of individual gene sequences. Sequences sampled from within a species form a within-species tree. The common ancestors of each within-species tree form a between-species tree. A detected difference counts as a polymorphism or a fixed difference depending on where it occurs in the phylogenetic tree. The test uses the numbers of polymorphisms and fixed differences as indicators of evolutionary rates. By directly comparing the numbers of detected differences the test indirectly compares the rate of evolution on the between-species tree with the rate on the three within-species trees. This comparison also assumes that if mutations occur in any lineage then they will occur at different sites. (More formally, the test assumes the infinite sites model. The infinite-sites model assumes that each mutation occurs at a new site so as to exclude the problem of multiple hits. When dealing with a slice of evolutionary time and sequences of some specifiable length such that the chance of the same site randomly mutates twice in that time is negligible, the infinite-sites model is a good approximation of the evolutionary process.)
2. A mutation whose fixation is independent of natural selection is termed a neutral mutation. If the frequency of neutral nutation is low, there are likely to be very many neutral networks comprising a few, or even single genotypes.
See:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16552/Good luck
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