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Hey guys I have a question. I am researching phylogenies and I am wondering, are these phylogenies based from theoretical silent mutations (i.e. genetic drift,mutation,etc)?
(Not exactly my field, but . . .) I'm not sure exactly what you mean by basing a phylogeny on silent mutations. Phylogenies are based on comparisons of DNA sequence between organisms. The particular sequence chosen can be nonfunctional, in which case all mutations are neutral, or it can be functional (a gene, generally), in which case many mutations will be deleterious. Neutrally evolving sequences change too fast to be useful for any kind of deep phylogeny, so most phylogenies use genes, since these are kept from varying too fast by natural selection.