PPT-Synonymous Codon Pattern of

Cauliflower Mosaic Virus in phylogeny and evolution Multiple sequence alignment Sequence Acquisition Isolates from Irananin Japanese American European Isolates from Grecian Turkish Iranian . ARCAIR IS SYNONYMOUS WITH CARBON ARC GOUGING The vast majority of observed sequence differences between members of a population are neutral (or close to neutral). These differences can be fixed in the population through random genetic drift. Some mutations are strongly counter selected (this is why there are patterns of conserved residues). Only very seldom is a mutation under positive selection. . Comparative Genomics. 18. th. -21. st. of February 2013. Lecture . 4. Positive selection. What is positive selection?. Positive selection is selection on a particular trait. - and the increased frequency of an allele in a population. Neutral Selection. Codon Degeneracy. Synonymous vs. Non-synonymous . dN/dS ratios. Why Selection?. The Problem. What does selection “look” like?. Yokoyama S et al. PNAS 2008;105:13480-13485. When moving into new dim-light environments, vertebrate ancestors adjusted their dim-light vision by modifying their . Gamma = 1 . no alignment – true homologous positions. with muscle alignment. log. 10. (x). LBA. phyml. no-alignment. A. C. D. B. still resolved by ml . Types of Mutation-Substitution. Replacement of one nucleotide by another. 50 replicates. s>0. Time till fixation on average: . t. av. = (2/s) ln (2N) generations . . (also true for mutations with negative . “. s. ”. ! discuss among yourselves). E.g.:  N=10. 6. , . Selection. Allele frequency. 0. 100. advantageous. disadvantageous. Modified from from . www.tcd.ie/Genetics/staff/Aoife/GE3026/GE3026_1+2.ppt. . Purifying selection in GTA genes. dN/dS <1 for GTA genes has been used to infer selection for function. Codon usage bias or CUB, a phenomenon in which synonymous codons are used at different frequencies, is generally believed to be a combined outcome of mutation pressure, natural selection, and genetic drift.. (1 980) Divergence” (PCD) the four kinds of be equal, as in studies, however, have actual substitution kinds of nucleotide mutation matrix codon substitution trix. For that the relative rates fo Most of the town residents are voting against the transportation proposal because they see public transit and crime as . synonymous. .. Because the athlete has led his team to four national championships, his name has become . The vast majority of observed sequence differences between members of a population are neutral (or close to neutral). These differences can be fixed in the population through random genetic drift. Some mutations are strongly counter selected (this is why there are patterns of conserved residues). Only very seldom is a mutation under positive selection. . Selection. Allele frequency. 0. 100. advantageous. disadvantageous. Modified from from . www.tcd.ie/Genetics/staff/Aoife/GE3026/GE3026_1+2.ppt. . Purifying selection in GTA genes. dN/dS <1 for GTA genes has been used to infer selection for function. Il codice genetico è DEGENERATO. Because of the degeneracy of all genetic codes, . 18-20 amino acids . are encoded by . more than one codon (2, 3, 4, or 6). .. If synonymous mutations are . strictly neutral. 18. th. -21. st. of February 2013. Lecture . 4. Positive selection. What is positive selection?. Positive selection is selection on a particular trait. - and the increased frequency of an allele in a population.