By Yi-Kuo Yu, Ralf Bundschuh, Terence Hwa (auth.), Michael Lässig, Angelo Valleriani (eds.)
This set of lecture notes supplies a primary coherent account of a singular point of the residing global that may be referred to as organic info. The e-book offers either a pedagogical and state-of-the paintings roadmap of this quickly evolving zone and covers the full box, from info that is encoded within the molecular genetic code to the outline of large-scale evolution of complicated species networks. The publication will turn out important for all those that paintings on the interface of biology, physics and knowledge science.
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Extra info for Biological Evolution and Statistical Physics
One observes a strong inﬂuence of genome size on the degree of anticodon redundancy and degeneracy. Small genomes tend towards redundancy, whereas large genomes favor degeneracy. The degree of redundancy at one extreme and degeneracy at the other, more or less spans the theoretical range. Mitochondria decode all codons with around 22 unique tRNAs not counting copies of the same anticodon. In order to do so mitochondria have evolved special redundant mechanisms of translation and have zero degeneracy.
The score of the MSA is then the sum of the scores of its columns. We seek a set of Pˆ maximizing d(Pˆ1 [j], . . , Pˆk [j]), D(A) = j for column scoring function d(·). The choice of the column scoring function, d(Pˆ1 [j], . . , Pˆk [j]), should reﬂect the application of the alignment. Residues that maximize d(Pˆ1 [j], . . , Pˆk [j]) should belong together. Note that in our formulation, the scores of columns are completely independent. However, in some formulations, the cost of a gap might depend on the length of the gap in many ways.
The tree is not parsimonious: Sequence data are not generally parsimonious, especially between distantly related sequences. , A → C vs. , A → C vs. , A → C → A), can all obscure the evolutionary history of a sequence. Convergent evolution results in a situation where the parsimony criterion will lead to the wrong tree model. Residues that appear to be closely related may simply be similar due selective pressure because they perform the same function. An example of this occurs in cows and colobine monkeys, species that independently evolved foregut fermentation .