MM Pe 291205
MM Pe 291205
MM Pe 291205
phylogenetics - pattern
2 - mechanism for this modification is natural selection
Population genetics
interested in genetic variation - understand generation and maintenance initially (until 1960s) only able to study indirectly - phenotype paucity of data led to controversy on the extent of genetic variation Classic school - very little genetic variation, cost associated with natural selection Muller Balance school - lots of genetic variation maintained by natural selection Dobzhansky
debate settled with advent of molecular approaches (direct) to the study of genetic variation - electrophoresis, sequencing tremendous amount of genetic variation exists thought was that this variation was maintained by natural selection accumulation of adaptively advantageous variants heterozygote advantage or heterosis
J.L. King & T.H. Jukes (1969) Non-Darwinian evolution. Science 164: 788
Note that many genetic changes have no effect on organismic fitness they are neutral Natural selection can not alter changes that it can not perceive Marshall biochemical evidence in support of these assertions e.g. synonymous substitutions, functionally equivalent cytochrome c variants, rapid evolution of fibrinopeptides (removed from functional fibrinogen)
huge debate ensued between selectionists (believe that extensive variation is a product of natural selection) and neutralists (believe that variation is a product of random fixation of neutral variants)
GAT AAC ATC CAA GGA ATA ACT GCA ATC GAC AAC ATC CAA GGT ATC ACG GCT ATC Asp Asn Ile Gln Gly Ile Thr Ala Ile
in virtually every gene ever studied synonymous sites change at a higher rate than nonsynonymous sites
The relative levels for these rates indicate the mode of selection for a gene Neutral evolution (no selection): Purifying selection: Diversifying selection: Ks Ka Ks >> Ka Ks << Ka
Exercises
Compare synonymous and nonsynonymous substitution rates for: 1 the Drosophila alcohol dehydrogenase (Adh) gene dros-adh.meg 2 the human & mouse gene pair mammal.meg Determine the mode of selection acting on each based on these rates 1 - load alignment into DnaSP 2 - assign coding region 3 - calculate Ks and Ka and compare (which is higher) 4 - load alignment into Mega 5 - calculate ds and dn and compare (which is higher) 6 - do statistical test for difference between ds and dn (see appendix II slide # 11)
(se(ds)
+ se(dn)2)