Population Genetics

1. Population Genetics • What is population genetics? • Studying Variation • Gene frequencies & allele frequencies • Hardy-Weinberg equilibrium • Factors that change allele frequencies in populations

2. I. What is Population Genetics • Goal: understand the genetic composition of a population and the forces that determine and change that composition • Fundamental measurement = allele frequency • Forces that change allele frequency = mutation, selection, gene flow, genetic drift Side-blotched lizards (Uta stansburiana) in central California experience unusual patterns of throat color.

3. Terms for understanding genetic diversity • Population, subpopulation, local population • Genetic structure = genetic composition of a given population • Based on analysis of Polymorphic loci • Only an estimate at that given moment in time • Genotype frequency = # individuals with a particular genotype in a pop / N • Allele frequency = # of copies of an allele in a pop / total # alleles in a pop.

4. Genetic Polymorphism Genetic Structure Allele Frequency

5. Gene Frequencies & Allele Frequencies • Gene frequency refers to proportion of particular allelic form among all copies of gene in population • Usually estimated by sampling population • diploid: 2 copies of gene • homozygotes: 2 copies of allele • heterozygotes: 1copy of each allele • haploid: 1 copy of allele • For two alleles, p + q = 1, where p and q are frequencies of the two alleles

6. Calculating Genotype Frequencies Relative frequencies of genotypes – proportion of organisms that have the particular genotype • The proportion of individuals in a population with a particular genotype • fA/A = # of A/A divided by the total • fA/a = # of A/a divided by total • fa/a = # of a/a divided by total

7. Calculating allele frequencies • If fA/A, and fa/a are the proportions of the three genotypes at a locus with two alleles, then the frequency p(A) of the A allele and the frequency q(a) of the a allele are obtained by counting alleles: • p= fA/A + ½ fA/a • q = fa/a + ½ fA/a • p + q = fA/A + fa/a + fA/a = 1.00 • q= 1 – p and p = 1 – q

8. Allele Frequency of A = 127/200 = 0.635 p(A) = 0.635 Allele Frequency of a = 73/200 = 0.365 q(a) = 0.365 = 1 - p

9. Mendelian considerations in population genetics…

11. II. Hardy Weinberg equilibrium • Sexual reproduction does not cause a constant reduction in genetic variation in each generation; rather the amount of variation remains constant generation after generation in the absence of other disturbing forces. • Model that shows what happens to allele and genotype in an “ideal” population using a set of simple assumptions

12. Populations in HW equilibrium have the following properties: • The frequency of alleles does not change from generation to generation • After one generation of random mating, offspring genotype frequencies can be predicted from the parent allele frequencies • Why use HW? It Identifies the real-world forces that change allele frequencies

13. 80% of all the gametes in the population carry a dominant allele for black coat (B) and 20% carry the recessive allele for gray coat (b). Random union of these gametes will produce a generation: p2 = 0.64 2pq = 0.32 q2 = 0.04 So 96% of this generation will have black coats; only 4% gray coats. Will the gray phenotype eventually be lost?

14. Testing for equilibrium • Determine the genotype frequencies • Directly from phenotypes • Analyzing DNA sequence • Calculate allele frequencies • Predict the offspring’s genotype frequencies using HW principle… does the prediction hold true? Are they similar to the observed frequencies?

15. CCR5 genotype example • N = 238 • 223 – 1/1, 57 – 1/Δ32, 3 - Δ32/Δ32 • f(1/1) = 0.788, f(1/Δ32) = 0.201, f(Δ32/Δ32) = 0.011 p = 0.89 q = 0.11 Expected genotype frequency: p2 = 0.792 2pq = 0.196 q2 = 0.012

16. The allele frequency for hemophilia (A) is 1/10,000 or 0.0001. • What is the allele frequency for the normal allele in the human population? • Among males, what is the frequency of affected individuals? • Within a population of 100,000 people, what is the expected number of affected males? What is the number of expected carrier females?

17. III. Factors that change allele frequencies in populations: Disturbing forces • Mutation • Non-random mating • Gene flow • Genetic Drift • Natural selection

18. 1) mutation • Mutation is the Ultimate source of variation, playing a fundamental role in the process of evolution • Mutation rate (μ)= probability that a copy of an allele changesto some other allelic form in one generation • Δq = μp • p = 0.8, q = 0.2, μ = 10-5, • Δq = (10-5)(0.8) = 0.000008) • Next generation: • qn+1 = 0.2 + 0.000008 = 0.20008 • pn+1 = 0.8 – 0.000008 = 0.799992 • Mutations don’t significantly alter allele freq. In 1 generation… • Gets slower every generation

19. 2) Gene flow • Gene Flow = migration • Gene flow - Genetic exchange between populations due to the migration of individuals between populations • Can offset the effects of genetic drift • Inhibited by isolation

20. 3) Genetic Drift • Genetic Drift • Random fluctuations of allele frequencies between generations • compounded by small population size • alleles can become fixed

21. The genetic bottleneck effect Founder effect, similar outcome… due to chance, the allele frequency in the founding population may differ from the original population.

22. 4) Inbreeding (non-random mating) • Inbreeding = Mating between relatives • IDB – identical by descent, the two alleles may be copies of the same gene in an earlier member of the line

23. 5) Natural selection • The force that can result in adaptation! • Darwinian fitness – relative probability of survival and rate of reproduction of a phenotype or genotype • Differential rates of survival and reproduction • Fitness is a consequence of the relation between the phenotype of the organism and the environment in which it lives, so the same genotype will have different fitnesses in different environments • consequence of relationship between phenotype and environment • same genotype may have different fitness in different environments

24. Heritability of beak depth in medium ground finches. The red line and circles are data from 1978, and the blue line and circles are from 1976 data. The results from the two years are consistent. Both show a strong relationship between the beak depth of parents and their offspring

25. In every natural population studied, more offspring are produced each generation than survive to breed. The reproductive capacity or biotic potential of organisms is astonishing (Table 3.1). It has been shown that in most populations, some individuals are more successful at mating and producing offspring than others. Variation in reproductivesuccess represents an opportunity for selection, as does variation in survival.

26. Combining forces shape genetic structure • Natural selection, mutation and genetic drift all can combine to maintain allele frequencies • Populations undergo evolution, not individuals • "Evolution is evidenced by changes in the gene pool which includes all the genes of any population at any give time."