Evolutionary Biology: Genes and Genomes

The Evolution of Genes and Genomes

• The birth of a gene can occur through duplication, which is the most common way new genes arise in eukaryotes, caused by unequal crossing over, replication slippage, or retrotransposition.
• Copy number variation occurs when a chromosome with a new gene duplicate spreads through a population, resulting in polymorphism in the number of copies of the gene that individuals carry.
• Gene duplication plays a key role in genome evolution, with 1% of human genes duplicated every million years, resulting in 1400 duplicates fixed in humans or chimpanzees since their common ancestor 7 million years ago.

Gene Structure

• Repeated domains arise from the duplication of a gene in a remote ancestor that coded for only a single domain.
• Exon shuffling occurs when mixtures of exons from genes with different functions generate new genes with new functions.

Evolution of Genome Size and Content

• Tetraploids can arise through whole genome duplication (autopolyploid) or hybridization of two species (allopolyploid).
• Horizontal gene transfer (HGT) occurs between distantly related organisms, allowing them to acquire new genes, including those that confer antibiotic resistance.

Gene Families

• A gene family is a set of loci that arose by duplication and code for proteins with similar biochemical functions.
• Paralogs are two or more genes that originated by duplication.

The Death of a Gene

• A pseudogene is a nonfunctioning duplicate that is fixed in the population, becoming a genetic skeleton useful for evolutionary biologists.
• Gene conversion occurs when a mutation in one locus is copied to another locus.
• Neofunctionalization occurs when a duplicate evolves a novel biological function.
• Subfunctionalization occurs when a duplicate gene and its parental copy carry out only some of the roles that the ancestral gene performed.

Evolution of Protein-Coding Genes

• Evolution of coding regions occurs through genetic drift, where most mutations that change the amino acid sequence are deleterious and removed by purifying selection.
• Neutral Theory of Molecular Evolution proposes that synonymous mutations evolve largely by random drift.
• Evolution of coding regions can also occur through positive selection, where natural selection favors changes to a protein, such as in the origin of the RNASE1B gene in the douc langur.
• Codon bias occurs when different codons corresponding to the same amino acid appear at different frequencies in the genome, caused by mutation or selection favoring codons that produce messages with fewer translation errors.