MODULE 5: Mutation, New Alleles, New Genes & Allele Frequencies

New alleles

Altered versions of existing genes that arise through mutation.

New genes

Genes that originate through duplication, retroposition, inversions, or whole genome duplication.

Mutation

A change in the nucleotide sequence of the genome; the ultimate source of all new alleles.

Coding vs. noncoding regions

Coding regions (exons) determine amino acid sequence; noncoding regions include introns and regulatory sequences that can still affect phenotype.

Synonymous mutation

A mutation that does not change the amino acid sequence of a protein due to redundancy in the genetic code.

Nonsynonymous mutation

A mutation that changes the amino acid sequence of the encoded protein.

Primary causes of point mutations

Random errors in DNA replication or DNA repair.

Factors influencing mutation rate

Mutagens, generation time, number of germline replications, and gene expression patterns.

Average number of new mutations in humans

Approximately 36-200 new mutations per individual.

Fitness effects of mutations

Most mutations are deleterious, some neutral, and few are beneficial.

Gene duplication (unequal crossing-over)

A mechanism where misaligned chromosomes create duplicated genes that can evolve new functions.

Retroposition

Formation of a new gene when mRNA is reverse-transcribed and inserted back into the genome.

Chromosome inversion

Chromosomal segment flips orientation; genes within the inversion become linked and inherited together.

Whole genome duplication (polyploidy)

Duplication of the entire genome; common in plants and can create new species and opportunities for new gene functions.

Example of gene family from duplication

The globin family, where multiple alpha- and beta-like globins evolved via repeated duplications.

Allozymes

Enzymes encoded by different alleles at the same locus.

Isozymes

Enzymes with the same function encoded by different loci (gene duplication origin).

Advantage of DNA sequencing

Detects all types of genetic variation, including synonymous and non-size-based differences.

Allele frequency

The proportion of a specific allele in a population, calculated from genotype counts.

How to calculate allele frequencies

Count total copies of each allele from genotypes, divide by total number of alleles in the population.

Example: A allele count in 80 AA + 40 Aa individuals

AA contributes 160 A alleles; Aa contributes 40 A alleles; total A = 200.

Example: a allele count in 40 Aa + 80 aa individuals

Aa contributes 40 a alleles; aa contributes 160 a alleles; total a = 200.

Allele frequency result for A and a (from example)

p(A) = 0.5 and q(a) = 0.5.

Environmental cline in allele frequency

A gradual change in allele frequencies across environmental gradients, indicating local adaptation.

Spatial variation in allele frequencies

Allele frequencies differ between geographic locations (e.g., beach mice coloration).

TLR variation in human populations

Immunogene alleles vary by region; some associated with disease resistance like malaria.

Mutation as a process

Mutation is random with respect to fitness but essential as the source of new genetic variation.

Mutation and selection interaction

Mutation creates variation; selection acts on beneficial mutations to drive adaptation.