module 3: molecular evolution

What is molecular evolution?

Evolution at the level of nucleic acids and proteins. It occurs due to changes in genome sequence and thereby in proteins.

What is a genome?

The complete set of genetic information in an organism. In eukaryotes, it is linear chromosomes; in bacteria and archaea, it is circular; viruses can be either.

What is the organization of a typical eukaryotic genome?

• Exons: Protein-coding sequences

• Introns: Non-coding sequences within genes

• Intergenic space: Non-coding sequences between genes

What percentage of the human genome is protein-coding?

Approximately 1.5%.

What are homologous genes?

Genes that share similarity due to common ancestry.

What are orthologous genes?

The SAME gene in different species (or individuals). They arise due to speciation events and provide information about evolutionary history. Most useful for inferring evolutionary history.

What are paralogous genes?

Genes that are COPIES of each other (in the same species or in different species). They arise due to duplication events.

Which type of homologous gene is most useful for inferring evolutionary history?

Orthologous genes, because they are the same gene diverging due to speciation events.

Why must you be sure two genes are orthologous before comparing their sequences?

Because paralogous genes may have different functions and evolutionary histories, making comparisons misleading.

What are synonymous substitutions?

Changes in DNA that do NOT change the amino acid/protein sequence due to the redundant genetic code. Usually considered neutral (not under selection).

What are non-synonymous substitutions?

Changes in DNA that DO change the amino acid. May be adaptive, deleterious, or neutral.

What are non-coding substitutions?

Changes in non-coding DNA. Usually no effect on protein, so considered neutral. May affect expression level (adaptive or deleterious).

Why are changes to the 3rd base pair most likely to be synonymous?

Because of the redundancy (wobble) in the genetic code—the 3rd position often does not affect which amino acid is added.

Why are changes to the 1st and 2nd base pairs least likely to be synonymous?

Because these positions are more critical for determining the amino acid.

Which codons can never have a silent mutation?

Start codon (methionine, AUG) and tryptophan (UGG).

What is a silent mutation?

A point mutation that does NOT impact the amino acid added to the protein.

What is a missense mutation?

A point mutation that leads to the WRONG amino acid being added to the protein. Normally harmful but can occasionally be beneficial.

What is a nonsense mutation?

A point mutation that leads to the generation of a STOP codon, resulting in a non-functional protein.

What are single nucleotide polymorphisms (SNPs)?

Changes in a single base pair. Might not lead to a change in protein or phenotype (silent mutation).

What are the types of SNPs?

• Non-coding region

• Coding region (synonymous or non-synonymous)

• Non-synonymous (missense or nonsense)

What is the Selectionist theory?

All genetic variation is due to natural selection. Mutations have a beneficial or deleterious effect, and natural selection is the dominant driver of evolution via DNA sequence change.

What is the Neutral theory?

Most mutations have no effect. Genetic drift is the dominant evolutionary force.

What is the Nearly-Neutral theory?

Most mutations have a small beneficial or deleterious effect. Population size affects the relative importance of selection vs. genetic drift as a driver of evolution.

What is the rationale for the nearly-neutral theory?

Large populations: high competition increases selection. Small populations: less competition, random loss of alleles more likely.

What is the importance of the neutral theory?

It provides a null hypothesis—if we can find substitutions that evolve neutrally, we can test whether other substitutions occur at that rate.

What does Ka represent?

Non-synonymous substitutions per non-synonymous site (protein evolution rate).

What does Ks represent?

Synonymous substitutions per synonymous site (neutral rate).

What does Ka/Ks > 1 indicate?

Positive (adaptive) selection—more amino acid changes than neutral changes (faster than neutral).

What does Ka/Ks < 1 indicate?

Purifying selection—fewer amino acid changes than neutral changes (slower than neutral).

What does Ka/Ks = 1 indicate?

Neutral evolution—amino acid changes occurring at the same rate as neutral changes.

How do you calculate Ka/Ks?

Ka = non-synonymous substitutions / non-synonymous sites. Ks = synonymous substitutions / synonymous sites. Then divide Ka by Ks.

What are the three possible fates of duplicated genes?

1. Pseudogenization: Duplicate gene is inactivated (most common)

2. Sub-functionalization: All gene copies lose some function

3. Neo-functionalization: New function for duplicate gene

What are transposable elements?

Pieces of DNA that replicate and insert themselves in new places ("selfish DNA"). They explain most of the variation in genome size across eukaryotic genomes.

What are the two types of transposable elements?

• Transposons: Move or copy via DNA

• Retrotransposons: Move or copy via RNA (using reverse transcriptase)

Who discovered transposable elements?

Barbara McClintock, studying corn. She was the first woman to win a solo Nobel Prize (1983).

How do transposable elements explain speckled corn kernels?

Pigment changes in developing corn kernels result from genes moving around (transposable elements inserting into pigment genes).

Why is there a discrepancy between genome size and gene number in eukaryotes?

1. Pseudogenes (inactive copies)

2. Introns ("junk DNA")

3. Transposable elements (selfish DNA)

How can molecular evolution be used to quantify time since population separation?

Neutral and nearly neutral polymorphisms accumulate at a predictable rate. By quantifying the number of polymorphisms, you can estimate time since populations separated.

How can molecular evolution be used to quantify migration among populations?

Large whole-genome differences indicate low migration without selection. Similar habitat and region-specific differences indicate selective pressure.

What is the "footprint" of random genetic drift?

Genome-wide reduction in polymorphism (nucleotide differences)—a "global effect."

What is the "footprint" of natural/sexual selection?

Reduced polymorphism in a gene region only—a "regional effect" impacting specific genes.