MODULE 8: Linkage, Recombination, Sex & Evolution at Multiple Loci

Linkage

Genes located on the same chromosome that tend to be inherited together.

Haplotype

A combination of alleles at multiple loci on the same chromosome (e.g., AB, Ab, aB, ab).

Linkage equilibrium (LE)

When alleles at two loci are independently associated; haplotype frequencies match allele frequency products.

Linkage disequilibrium (LD)

Non-random association of alleles at different loci; certain alleles occur together more often than expected.

Coefficient of LD (D)

D = fAB·fab – fAb·faB; measures deviation from linkage equilibrium.

Interpretation of D

D = 0 means loci in equilibrium; D ≠ 0 means linkage disequilibrium.

Effect of recombination on LD

Recombination reduces LD each generation: D' = D(1 – r).

Causes of LD

Selection on multilocus genotypes, genetic drift, and population admixture (migration or hybridization).

Genetic hitchhiking

When an allele increases in frequency because it is linked to a positively selected allele.

Selective sweep

A region of the genome where variation is reduced due to hitchhiking with a strongly selected allele.

Cost of sex

Sexual reproduction halves gene transmission, requires finding mates, increases risks, and requires complex structures/behaviors.

Benefit of sex

Recombination creates new haplotypes, reduces LD, and restores genetic variation each generation.

Muller’s ratchet

Asexual populations accumulate harmful mutations over time because they cannot recreate mutation-free genotypes.

Why sex helps purge mutations

Recombination can generate mutation-free chromosomes, allowing selection to remove deleterious alleles.

Sex and environmental change

Sex helps populations adapt faster by generating rare, advantageous multilocus genotypes.

Red Queen hypothesis

Hosts must constantly generate new genotypes via sex to keep up with rapidly evolving parasites.

Prediction of Red Queen model

Sexual reproduction should be most common where parasite pressure is high.

Evidence for Red Queen

C. elegans experiments and Potamopyrgus snails show higher sexual reproduction in high-parasite environments.

Multilocus evolution

Evolution at two or more loci depends on both allele frequencies and haplotype frequencies.

Why multilocus models matter

Selection at one locus can affect allele frequencies at linked loci when LD is present.

Population admixture and LD

When genetically distinct populations mix, they produce LD even if loci were in equilibrium previously.

Effect of distance between loci on LD decay

Closer loci (low recombination) retain LD longer; distant loci lose LD faster.