Bio 2 - evolution of genes & genomes

DNA records evolutionary history

- mutations create the variation needed for evolution

- when lineages split, their DNA starts to diverge

mutations create the variation needed for evolution

evolution leaves measurable signals in DNA sequences

when lineages split, their DNA starts to diverge

more time since divergence= more sequence differences

differences in DNA accumulate after...

species diverge

sequence comparisons reveal...

evolutionary changes in genes & proteins

homologous sequence

sequence shared among species due to common ancestry (even if the sequence has changed over time)

- more time since divergence= more sequence differences

- sequences in DNA or proteins allow us to study their evolution

Sequence Alignment

allows us to compare homologous DNA positions across organisms & identify evolutionary changes

# of changes among homologous sequences are underestimated bc of...

- multiple substitution

- coincident substitution

- parallel substitution

- back substitution

by comparing DNA sequences...

we can trace lineage divergence & build phylogenetic trees that reveal evolutionary history

synonymous substitutions

no phenotypic effects

- neutral to natural selection, so they accumulate over time

nonsynonymous substitutions

alter protein function

- most are deleterious

- some neutral

- some beneficial

rates of nonsynonymous substitution are typically...

much lower than rates of synonymous substitution in functional genes

comparing nonsynonymous to synonymous substitution rates reveals...

whether a gene is neutral, under purifying selection, or under positive selection

detecting natural selection in DNA

ratio of nonsynonymous to synonymous substitutions (dN/dS)

neutral evolution

mutations spread or disappear by chance (dN/dS is close to 1)

Positive selection

natural selection favors a beneficial mutation (dN/dS is >1)

purifying selection

natural selection removes harmful mutation (dN/dS is

different codons within the same gene can experience...

different modes of natural selection

similarity matrix

aligned sequences can be summarized using a similarity matrix that counts similarities & differences between species & estimate dN/dS

in immune genes most codons experience...

purifying selection, but pathogen binding sites experience positive selection

large scale genome changes

- point mutations often create small-scale changes to existing genes

- large scale genome changes can add new genetic material (ex: gene duplication events)

gene duplication events produce spare copies of functional genes...

the new copies can have different fates

- retain same fxn

- diverge in expression

- gain a new fxn

- decay as a pseudogene

whole genome duplications (polyploidy events)

simultaneously create an extra copy of 1000s of genes

lateral gene transfer

occurs when genetic material moves between species introducing novel functions that can rapidly alter evolutionary trajectories