Biological Evolution and Statistical Physics by Yi-Kuo Yu, Ralf Bundschuh, Terence Hwa (auth.), Michael

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 unique point of the dwelling international that may be referred to as organic info. The e-book provides either a pedagogical and state-of-the paintings roadmap of this speedily evolving quarter and covers the full box, from details that's encoded within the molecular genetic code to the outline of large-scale evolution of advanced species networks. The booklet will turn out beneficial for all those that paintings on the interface of biology, physics and data science.

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A variant on tree alignment is star alignment (SA), in which it is assumed that the underlying tree is a star. , [9,10]). Altschul and Lipman [9] pointed out that SP, TA and SA costs for the same column can be very different, as shown in Fig. 2. SP overcounts mutations in a column because it considers that a separate mutation occurred between each pair in the column. In some sense, it is a “least parsimonious,” or profligate, model of mutation. In contrast, TA has been traditionally used with the maximum parsimony criterion.

In other species, lysozyme is only needed in the intestines. As a result, lysozymes in cows and colobine monkeys exhibit amino acid substitutions not found in other species, suggesting, wrongly, that the two species are closely related. This would result in the wrong tree for those residues. Tetraloops in rRNA provide another example of convergent evolution [43,44]. Tetraloops are strings of six bases that form loops at the end of helices in rRNA structures. The two end bases bond, allowing the internal four bases to form a loop.

Because the codon abundance of the parasite can differ from that of the host, the host can to a certain extent control the replication of parasites in its cells. Our model allows us to infer the consequences of redundancy and degeneracy on the translation rate of parasite genomes. We now distinguish between parasite and host codon usage. Let the m × 1 → vector − cp contain the abundances of codons in the parasite genome. The first step in translation is the transcription into mRNA, which is a possible source of error.

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