lecture 5- molecular evolution preview

Synonymous substitution

A nucleotide change that does not alter the amino acid; typically neutral.

Nonsynonymous substitution

A nucleotide change that alters the amino acid; may be deleterious, neutral, or advantageous.

Neutral mutation

A DNA change with no effect on fitness; frequency changes due to drift.

Neutral mutation accumulation

Neutral mutations accumulate over time at a constant rate, forming a molecular clock.

Neutral mutation rate

Independent of population size; rate of fixation equals mutation rate (μ).

Positive selection

Occurs when nonsynonymous substitutions outnumber synonymous ones.

Purifying selection

Occurs when synonymous substitutions outnumber nonsynonymous ones.

Neutral selection

Synonymous ≈ nonsynonymous substitutions; no selective forces at play.

Fixation probability

The chance a neutral allele becomes fixed = its current frequency.

Rate of fixation (neutral mutation)

Equal to the neutral mutation rate (μ), independent of population size.

Molecular clock

A tool that uses constant neutral mutation rates to estimate divergence times.

Pseudogenes

Nonfunctional gene copies with high substitution rates due to lack of constraint.

Genome size variation

Results from differences in noncoding DNA amounts across taxa.

Human genome

~3 billion base pairs, ~22,000 genes; only 3% codes for proteins.

Noncoding DNA

Includes pseudogenes, regulatory elements, transposons; may affect gene expression.

Genome organization

Refers to arrangement and proportion of coding vs. noncoding regions.

Lateral gene transfer

Genes acquired from other species, increasing genetic variation.

Gene duplication

Creates genetic novelty; duplicated genes can evolve new functions.

Sexual reproduction

Generates genetic variation through recombination and independent assortment.

Transposons

Mobile DNA elements that can influence gene expression and genome structure.

Endogenous retroviruses

Ancient viral sequences embedded in the genome; ~5–8% of human genome.

Population size effect

Large populations purge slightly deleterious noncoding DNA more efficiently than small populations.

Genome complexity

Not always correlated with gene number; influenced by noncoding DNA.