population genetics emerged in the 1920s founders: r.a ... 2015/population genetics for...

Population Genetics

Emerged in the 1920s Founders: R.A. Fisher, Sewall Wright, J.B.S. Haldane Provided the mathematical foundations for the evolutionary process Also important in: e.g. Agriculture, medical and human genetics, bacterial resistance, evolution of virulence

Population Genetics

What are the levels of genetic variation in populations? How do different mating patterns affect genotype and allele frequencies? What forces are responsible for changes in the genetic composition of populations? Mutation, Migration, Genetic drift, Natural selection

Phenotype M MN N TOTAL Genotype MM MN NN Obs # 180 240 80 500 Genotype 180/500 240/500 80/500 proportions = 0.36 = 0.48 = 0.16

1. Using the numbers of various genotypes observed in the population p = freq(M) = # of M alleles/total alleles = (2 x 180 + 240)/ (2 x 500) = 0.6 q = freq(N) = # of N alleles/total alleles = (2 x 80 + 240)/ (2 x 500) = 0.4 Note that the alleles frequencies p + q = 1 or you've made a mistake. 2. Using the proportions of each genotype. p = freq (MM) + 1/2 x freq (MN) = 0.36 + 0.48/2 = 0.6 q = freq (NN) + 1/2 x freq (MN) = 0.16 + 0.48/2 = 0.4

Genotype and allele proportions for the MN blood group polymorphism

Allozymes, gel electrophoresis and the “Find em and Grind em” era.

Alcohol dehydrogenase in pollen of Asclepias syriaca (milkweed)

Esterase in T. subulata

Glucose phospohate isomerase in autotetraploid T. subulata

Cleaved amplified polymorphism in style polygalacturonase

Schematic of allozyme gel electrophoresis showing an enzyme segregating for 3 alleles, F, M, S, in a population sample.

F M S

SS MS MM FS FM FF MS MM FS FM SS SS

See Fig 18-14 for view of SNP variation across a sample of humans. Note the different numbers of haplotypes.

Tristyly in Oxalis. Plants exhibit negative assortative mating

short-styled mid-styled long-styled S- -- ssM- ssmm

Allele frequency change due to mutation alone

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Generation

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Mutation B to b*

Mutation and the generation of linkage disequilibrium

Decay of linkage disequibrium with r = 0.5

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ABAbaBab

Begin with complete linkage disequilbrium with just AB and ab combinations of alleles at equal frequency and allow random mating and recombination with r = 0.5. Eventually there is decay of linkage diseq and we end up with equal freqs of AB Ab aB ab in the population. In subsequent slides, small r-values reduce rate of decay

Decay of linkage disequibrium with r = 0.1

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Decay of linkage disequibrium with r = 0.01

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Decay of linkage disequilibrium with r = 0.01

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0.61 14 27 40 53 66 79 92 105

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So even with a 1cm distance between genes and 200 generations the disequilibrium has not yet fully decayed