Lecture 3

Question 1

World has over 50,000 edible plants

Answer 1

• 3 species account for 60% of food energy intake: rice, maize, wheat
• Abundant genetic variation exist in wild ancestor of food crops

Question 2

Crop diversity

Answer 2

• Domestication of crops:
  
  • Severe bottleneck: only a tiny subset of individuals of wild population chosen to be cultivated
  • Strong artificial selection: Humans breed and retain best performing crop plants, selection on germination timing, seed size, nutrition

Question 3

Consequences of domestication

Answer 3

• Reduce genetic variation: fewer individuals contribute genes, less beneficial traits
• Measure:
  
  • H: average frequency of heterozygous individuals per gene locus
  • P: proportion of gene loci that are polymorphic
  • pi: average number of nucleotide differences per site for any randomly sampled pair of nucleotides

Question 4

Why do we care about crop genetic variation

Answer 4

• Clues to past artificial selection: what traits did our ancestors select
• Pest and pathogen management: can we reduce crop loss to pests
• Future improvement of crops: is it possible to keep breeding better crops without genetic engineering

Question 5

Domestication of maize from teosinte

Answer 5

• Domestication 10000-5000 years ago
• Application of artificial selection before discovery of genetics and natural selection

Question 6

Domestication lead to loss of variation

Answer 6

• Less variation in teosinte than maize

Question 7

Distinguishing bottlenecks from bottlenecks + selection

Answer 7

• Bottlenecks reduce effective population size (Ne)
• Ne is size of idealized population with same properties with respect to genetic drift and allele frequencies as observed population. Idealized is all inidviduals with equal opportunity to pass on their genes

Question 8

Effective population size

Answer 8

• Census size (N) = total number of adults in population
• Effective size (Ne) is number of adults that breed
• Effective size is most important for evolutionary analysis

Question 9

Why does N not equal Ne

Answer 9

• Stochastic differences in genetic contribution of individuals
• Unequal sex ratio
• Overlapping generations: mating between offspring and parents. Genetic similarities don’t pass to next generation
• Fluctuations in population size
• Consequently, number of individuals making genetic contributions to next generation is always lower than total census number of individuals

Question 10

N&raquo_space; Ne

Answer 10

• Happens in absence of selection
• Natural or artificial selection reduces Ne even further
• Ne measured as species average across genome
• Ne measured for each gene separately

Question 11

Results for maize and teosinte

Answer 11

• 2-4% of teosinte genome experiences strong artificial selection during domestication
• Some genes expected: genes for ear production, growth, morphological traits
• Some genes unexpected: 5 of top 30 are genes of unknown function

Question 12

Irish potato famine

Answer 12

• Potatoes do not grow easily from seed
• Sprout easily from underground tuber. Leads to clonal propagation
• Lumper variety: Large yield, lots of carbohydrates and lots of calories
• Only 1-3 genotypes of potato were cultivated and they were clonally propagated
• Phytophthora infestans is fungus like eukaryote -> potato yield fell drastically, rot in ground

Question 13

Implications

Answer 13

• Use evolutionary genetic principles to discover regions of genome under past artificial selection, improve future agricultural crops, design sensible planting schemes to reduce risk of monoculture devastation