module three: molecular evolution

Describe the organization of a typical eukaryotic genome in terms of coding and non-coding DNA.

• non-coding sequences: intergenic space, introns

• coding sequences: genes, exons

Define synonymous, non-synonymous, and non-coding DNA and explain how they can be used to infer evolutionary processes.

• synonymous: does NOT change the amino acid/protein sequence (neutral)

• non-synonymous: CHANGES amino acid (unpredictable effects)

• non-coding mutations: usually DOES NOT AFFECT

Define homologous, orthologous, and paralogous genes and explain which one is most useful for inferring evolutionary history.

• homologous genes: similarity due to common ancestry

• orthologous genes: shared gene in different species through speciation

• paralogous genes: shared genes in different species through gene duplication

Explain the rationale for the nearly-neutral theory and how it helps us detect selection for (or against) DNA variants.

Give examples of the three possible fates of duplicated genes and explain which is the most likely/common fate.

• pseudogenization: one copy is lost or loses function

• neofunctionalization: duplicate evolves new biological function

• subfunctionalization: duplicates split up the function of the original parent gene

Describe the contribution of transposable elements to genome variation.

Describe the DNA "footprint" that each evolutionary force leaves on genomic variation.

Compute Ka/Ks and interpret whether a region of DNA sequence is neutral, beneficial, or deleterious.