lecture 8: molecular evolution

c-value paradox

lack of correlation btwn complexity of organisms and genome size

why does the c-value paradox occur?

DNA between genes (“junk” DNA) makes up whole genome and can be any length for any species, but number of genes indicates complexity of organism

example of morphologically high similarity but genetically low similarity organisms?

living fossils have morphologically not changed over time (look the same as they always have), have very different genetics, very few genes that have evolved but not changed phenotype bc they’re so adapted. ex: coelacanth, horseshoe crab

example of morphologically low similarity but genetically high similarity organisms?

humans and chimps, distance between is less than between sibling species of drosophila, most sequenced proteins exhibit no difs in amino acids

molecular clock

zuckerkandl & pauling, from homologous amino acid sequences, assess relationship btwn estimated (from fossil record) protein divergence and evolutionary time

molecular clock relationship btwn synonymous and nonsynonymous mutations

molecular clock ticks at different rates for each

molecular clock conclusion

majority of evolution involves substitution of silent mutations, likely by random drift

neutral theory of molecular evolution: 1st criteria

most mutations are harmful and thus removed by “negative” (or “purifying”) natural selection

neutral theory of molecular evolution: 2nd criteria

some mutations are neutral and thus accumulate in natural pops by random genetic drift

neutral theory of molecular evolution: 3rd criteria

very rarely, beneficial mutations occur and are fixed by “positive” natural selection

neutral theory of molecular evolution: 4th criteria

The rate of evolution of a molecule is determined by its degree of “functional constraint”

neutral theory of molecular evolution: 5th criteria

neutral mutations and random genetic drift are responsible for virtually all molecular evolution

naturalist view of genome structure

studied natural pops, expected all genes to be perfectly adapted & fixed (single allele) under directional selection

mendelian view of genome structure

studied genetics exclusively in labs, all genes must be under balancing selection

classical view of genome structure

aka naturalist, most loci homozygous for wildtype alleles, polymorphism rare

balanced view of genome structure

aka mendelian, most loci heterozygous, polymorphism common

classical view on speciation

difficult, mutation limited

balanced view on speciation

easy, opportunity limited

classical view on selection

purifying

balanced view on selection

balancing

classical view on pop variation

inter > intra

balanced view on pop variation

intra > inter

classical view on polymorphism

transient, short lived

balanced view on polymorphism

balanced, long lived

mutations are either:

fixed between species OR polymorphic within species
silent OR replacement

what happens to mutations when selection is happening?

increase in changes of amino acids btwn species (mutations)

what happens to mutations when selection is NOT happening?

same # of silent and replacement mutations btwn species

mcdonald-kreitman test

polymorphic replacement mutations : polymorphic silent mutations = fixed replacement mutations : fixed silent mutations

ratio polymorphic = short term evolution

ratio fixed = long term evolution

when does positive selection occur?

when rate of replacement substitution exceeds rate of silent substitution

positive selection widely documented in which two classes of genes?

genes involved in host-pathogen interactions, genes functioning in reproduction

wright’s fixation index/F statistics

compares allelic freqs of 2 pops of same species

wright’s fixation index/F statistics: completely mixed pops

0, gene has same allelic freq

wright’s fixation index/F statistics: completely separate pops

1, gene is completely different, alleles are fixed

conclusion of wright’s fixation index/F statistics

natural selection may be more important in directing molecular evolution than previously believed