AP Syllabus focus:
‘Human-directed breeding in crops and domesticated animals alters allele frequencies and trait diversity within populations.’
Artificial selection in agriculture and domestication relies on humans controlling which individuals reproduce. Over generations, this shifts allele frequencies, reshapes trait distributions, and can both increase useful variation and reduce overall genetic diversity.
Core idea: how human-directed breeding changes populations
Human-directed breeding is a form of artificial selection in which selective pressures come from human goals (yield, temperament, appearance) rather than environmental survival challenges.
Artificial selection: Human-mediated selection in which individuals with desired heritable traits are preferentially bred, causing allele frequencies and phenotypes in the population to change over generations.
Key population-level outcomes:
Allele frequencies change because breeders increase reproduction of individuals carrying alleles linked to preferred traits.
Trait diversity shifts: some traits become more common; others may be lost if their alleles decline or are removed from breeding lines.
Effects accumulate across generations because only heritable variation responds to selection.
Mechanisms used in breeding programs
Choosing breeders (selection of parents)
Breeders identify individuals with desirable phenotypes, often based on measurable traits (e.g., milk yield, growth rate, grain size, disease resistance).
Directional selection is common: repeatedly choosing individuals at one end of the trait range.
This figure plots allele frequency () across generations under positive directional selection, illustrating how selection can drive a favored allele upward over time. The different curves show how dominance relationships change the rate at which allele frequencies shift, even when selection favors the same allele. It reinforces that artificial selection works by changing which genotypes contribute more offspring to the next generation. Source
Selection can be based on:
Visible phenotype (coat colour, fruit size)
Performance tests (egg production, feed conversion)
Family history/pedigree (tracking trait inheritance)
Controlled crosses and maintaining lines
Common strategies to increase desired trait combinations:
Inbreeding/linebreeding: mating related individuals to “fix” desired alleles and produce more uniform offspring.
Hybridisation: crossing genetically distinct lines to combine traits (e.g., stress tolerance + high yield).
Backcrossing: crossing offspring back to a parent line to retain most of the parent’s genome while introducing a specific allele/trait.
Because these approaches change who contributes gametes to the next generation, they directly alter the gene pool of the domesticated population.
Examples in plants and animals (what changes and why)
Crops
Human selection often targets traits that improve production and handling:
Larger fruits/seeds, reduced seed dispersal, uniform ripening
These photos illustrate seed shattering (natural seed dispersal) versus the non-shattering traits favored during crop domestication. Selecting plants that retain seeds longer increases harvestability and drives domestication-associated alleles to higher frequency in cultivated populations. This example makes the connection between a human farming goal and a predictable evolutionary response. Source
Resistance to pathogens or herbivores
Tolerance to drought, salinity, or cold These targets can increase the frequency of alleles that enhance yield or survivorship in managed fields, even if those alleles would be disadvantageous in the wild.
Domesticated animals
Selection commonly targets:
Behavioral traits (reduced aggression, increased docility)
Growth and reproduction (rapid weight gain, litter size)
Product traits (wool quality, milk yield) As preferred alleles rise in frequency, populations can become specialised for human-controlled environments.
Trade-offs and limitations (important AP Biology implications)
Reduced genetic diversity and vulnerability
Strong, repeated selection and small breeding pools can reduce variation:
Fewer alleles overall (loss of rare alleles)
Increased uniformity of phenotype This can make populations more vulnerable to:
New diseases (pathogens can spread rapidly through genetically similar hosts)
Environmental shifts (less standing variation to respond)
Inbreeding depression and harmful alleles
Inbreeding can increase homozygosity, which may expose deleterious recessive alleles, lowering fitness-related traits (fertility, survival, immune function).
This diagram contrasts homozygosity “by descent” versus “by state,” showing how inbreeding increases the probability that two alleles in an individual are inherited from the same ancestral copy. By making alleles more likely to be identical by descent, inbreeding raises homozygosity and can unmask recessive deleterious variants. The figure provides a mechanistic bridge between mating patterns and changes in genotype frequencies. Source
Breeding programs may counter this by introducing new genetic lines while trying to retain key selected traits.
Unintended correlated responses
Selecting for one trait can change others due to:
Pleiotropy (one gene influences multiple traits)
Genetic linkage (alleles inherited together) This can produce undesirable side effects (health issues, reduced robustness) alongside the desired phenotype.
FAQ
They use common-garden or standardised rearing conditions so phenotypic differences better reflect genotype.
They may also compare relatives (half-sib/full-sib designs) to estimate how consistently a trait is inherited.
Crossing inbred lines can increase heterozygosity, masking deleterious recessive alleles and improving performance.
In later generations, recombination breaks up favourable allele combinations, so the uniform “hybrid vigour” can decline.
Maintain larger breeding populations
Rotate or mix breeding lines
Introduce novel germplasm periodically
Use mating schemes that limit relatedness while retaining selected alleles
It uses DNA markers linked to target alleles to choose breeders without waiting for the full phenotype.
This is especially useful for traits expressed late in life or only under specific conditions.
Rapid selection can outpace compensatory physiology, and pleiotropy/linkage can couple desirable production traits with health costs.
Welfare issues can be reduced by selecting simultaneously for robustness traits (e.g., mobility, fertility) alongside production traits.
Practice Questions
Explain how human-directed breeding can change allele frequencies in a population of domesticated animals. (2 marks)
States that humans choose which individuals reproduce based on desired heritable traits (1).
Explains that preferred alleles are passed on more often, increasing their frequency over generations (1).
A crop-breeding programme repeatedly selects plants with the largest seeds and uses a small number of parent plants each generation. Describe how this could alter trait diversity in the crop population and give two biological risks associated with the approach. (5 marks)
Describes directional selection towards larger seeds, shifting the population mean (1).
Explains allele frequencies for large-seed alleles increase due to preferential reproduction (1).
Explains overall genetic/trait diversity may decrease because few parents contribute to the next generation (1).
Risk 1: reduced genetic diversity increases vulnerability to disease/environmental change (1).
Risk 2: increased homozygosity/inbreeding depression or fixation of harmful alleles/unintended correlated traits (1).
