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Adaptive Evolution • Most variation within or between species random fixation selectively neutral mutations. • Selectively deleterious purifying selection not tolerated. • Occasionally, mutations selective advantage positive selection (adaptive evolution) fixed in the population at a much higher rate. Why? • Can indicate which amino acid sites/domains are functionally important in a molecule • Interest in detecting whether most mutations are deleterious, advantageous or neutral • Identification of selected loci provide insight into the events that have shaped a species’ evolution & can indicate which genes have been particularly important in the evolution of a species. • By screening for selective signatures associated with immunity or disease susceptibility, we may be able to identify those genes that have been of critical importance to the development of disease resistance.
Amino Acid Sites Subject to Positive Selection in Mammalian a-Defensins Red: sites predicted to be under positive selection. Blue: sites that are 100% conserved across all OTUs. Lynn et al., MBE 2004.
Page 1: PAML Phylogenetic Analysis by Maxim
Page 5 and 6: Metodi di Maximum Likelihood • In
Page 7 and 8: Site-specific models Allow ω vary
Page 9 and 10: H 0: Beta distributed variable sele
Page 11 and 12: Requirements for PAML Analysis •
Page 13 and 14: Coding DNA sequence alignment in PA
Page 15 and 16: CODEML.ctl parameter file • Zihen
Page 17 and 18: Output Files Several different outp

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