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Variation

Variation. Chapter 9. Evolution is a two-step process. Variation arises among individuals The proportions of variant types change from generation to generation.

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Variation

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  1. Variation Chapter 9

  2. Evolution is a two-step process • Variation arises among individuals • The proportions of variant types change from generation to generation. • However, changes in the proportions of variants in one generation are not carried over to subsequent generations unless the variation is at least partly inherited.

  3. Some definitions: • Phenotype – • A morphological, physiological, biochemical, or behavioral characteristic of an individual organism • The way an organism “looks” • e.g. blue eyes, curled wings • Locus – • A site on a chromosome, or the gene that occupies that site

  4. Some more definitions: • Allele – • A particular form of a gene • e.g. A, a • Genotype – • The genetic constitution of an organism at one or more loci • e.g. Aa, aa

  5. Even yet still more definitions: • Genotype frequency – • The proportion of a population that has a certain genotype • Allele frequency – • The proportion of the copies of an allele in a population that are of that allelic type

  6. Distinguishing Sources of Phenotypic Variation • Genetic Differences • Environmental Differences • OR BOTH....

  7. Major Sources of Phenotypic Variation • Differences in Genotype Actual differences in DNA sequence at 1 or more loci • Differences in Environment (=non-genetic effects) -Physiological differences -Behavioral traits These differences can be affects due to environmental variables at many scales Maternal Effects (‘crack baby...) Exposure during early development etc...

  8. So... How Do We Separate Genetic vs. Environmental Causes of Variation? Very Difficult since many times variation is due to many genes. Therefore, simple Mendelian ratios are not often observed -Experimental Crosses -”Cross-Fostering” experiments (switching eggs between nests)

  9. So... How Do We Separate Genetic vs. Environmental Causes of Variation? Correlation between the average PHENOTYPE of offspring and that of their parents OR greater resemblance among siblings than among unrelated individuals suggests GENETIC variation contributes to PHENOTYPIC variation

  10. How do we measure genetic variation in a natural population? • Knowing how much genetic variation a population carries requires that we know what fraction of the loci are polymorphic, how many alleles are present at each locus and what their frequencies are.

  11. How do we measure genetic variation? • Look directly at proteins or DNA Sequences • Allozymes • Isozymes • DNA sequence • Microsatellites

  12. Tools • Gel electrophoresis • PCR • Automated DNA sequencing

  13. Determining Genotypes • Gel electrophoresis • DNA and proteins have charge • Apply electric current to samples and they migrate toward oppositely charged pole • Migrate according to size and mass • Differently sized alleles go different distances

  14. Gel electrophoresis

  15. Load Gel

  16. Run the Gel

  17. Take a Picture of the Gel DNA ladder Digested DNA Uncut DNA

  18. Determining Genotypes • Human gene CC-CKR-5 • Encodes for CCR5 cell surface protein receptor on helper T cells • When receptor senses pathogens, informs killer T cells to attack • HIV-1 uses CCR5 as coreceptor to bind with CD4 T cells

  19. Determining Genotypes • Human gene CC-CKR-5 • Some people are resistant to HIV-1 infection • They contain a 32 bp deletion in the CCR5 gene: D32 allele • Wild type allele: +

  20. Determining Genotypes • Human gene CC-CKR-5 • If homozygous dominant (+/+) they can be infected • If homozygous recessive (D32/D32) they cannot be infected • If heterozygous (+/D32) they can be infected but progress to AIDS more slowly

  21. Determining Genotypes • Human gene CC-CKR-5 • Researchers cut DNA with restriction fragments • Can determine a person’s genotype with simple electrophoresis

  22. Calculating Allele Frequencies • To determine how common an allele is can calculate its frequency • For example, 43 Ashkenazi people were tested • 26 were wild type (+/+) • 16 were heterozygous (+/D32) • 1 was homozygous recessive (D32/D32)

  23. Calculating Allele Frequencies • 86 allelic copies (43 indviduals) • 18 were D32 • 16 heterozygotes (½ 32) • 2 homozygote • 18/86 = 0.209 or 20.9% • Other races and/or nationalities have much lower rates of D32 alleles

  24. Calculating Allele Frequencies • 86 allelic copies (43 indviduals) • 68 were + • 16 heterozygotes • 52 homozygote • 68/86 = 0.791 or 79.1% • Frequencies of the two alleles should add to 1. (p + q=1)

  25. From Genotypes (43 individuals) (+/+) (D32/D32) (-/-)

  26. Homework: Calculate Allele Freq. for Thursday

  27. How Can We Quantify and Track Genetic Variation in Populations?

  28. Hardy-Weinberg Equilibrium Principle • Designed as a simple model to account for and estimate how alleles behave in populations • Develops a null model for behavior of genes in populations • Model specifies what will happen to frequencies of alleles and genotypes • Applies to all diploid sexual organisms

  29. Hardy-Weinberg Equilibrium Principle • Population = group of interbreeding individuals and their offspring • Life Cycle • Adults produce gametes • Gametes combine to make zygotes • Zygotes grow up to become next generation of adults • Track fate of Mendelian genes across generations in a population • Find out if particular alleles become more or less common over time

  30. Hardy-WeinbergExample: • Imagine that mice have a particular locus A with two alleles: A and a (Could also call them A1 and A2) • Track these alleles and follow them through one complete turn of the cycle to see if frequencies change

  31. Hardy-Weinberg Equilibrium Principle • A numerical example • Assume adults choose their mates at random • Matings are random within the gene pool • Diploid organisms (2N), so each has two alleles for the A locus • Meiosis (during gametogenesis) caused one allele (either A or a) to be in each gamete for the A locus

  32. Hardy-Weinberg Equilibrium Principle • A numerical example • Imagine 60% of eggs and sperm received allele A and 40% received allele a • Frequency of Aallele in gene pool is 0.6, of a allele is 0.4 • When egg and sperm meet, what proportion of genotypes will be AA? • 60% egg will be A, 60% sperm will be A: • 0.6 X 0.6 = 0.36 • 36% of zygotes will have genotype AA

  33. Hardy-Weinberg Equilibrium Principle • How many would be aa? • 0.4 X 0.4 = 0.16 • How many would be Aa? • 0.6 X 0.4 X 2 = 0.48 • Notice that 0.36 + 0.48 + 0.16 = 1 • All possible genotype frequencies will add up to one

  34. Hardy-Weinberg Equilibrium Principle • If zygotes grow up, what will the frequency of A in the next generation be? • AA is 36% • All gametes carry A • Aa is 48% • Half will carry A, half will carry a • aa is 16% • All gametes carry a • Frequency of Ain next generation will be: • 0.36 + (1/2)0.48 = 0.6 • Frequency of a will be: • 0.16 + (1/2)0.48 = 0.4

  35. Hardy-Weinberg Equilibrium Principle • A numerical example • 0.6 + 0.4 = 1 • Allele frequencies are the same as in the first generation • Allele frequencies are in equilibrium • The population does not evolve • If a population is in Hardy-Weinberg Equilibrium it will never evolve (=allele frequencies in pop. will NEVER change) • Regardless of starting frequencies

  36. Hardy-Weinberg Equilibrium Principle • The General Case • Imaginary population • Single locus with A and a as the alleles • Three possible diploid genotypes • AA, Aa, aa • Frequency of allele A is called p • Frequency of allele a is called q • p + q = 1 • (note: we could have called a=p and A=q, no difference!)

  37. Hardy-Weinberg Equilibrium Principle • The General Case • Let gametes make zygotes: • Four combinations • A + A = AA p X p = p2 • A + a = Aa p X q = pq • a + A = aA q X p = qp • a + a = aa q X q = q2 • p2 + 2pq + q2 = 1 • Genotype frequencies in Hardy-Weinberg Equilibrium

  38. Hardy-Weinberg Equilibrium Principle • Two fundamental conclusions • Conclusion 1: the allele frequencies in a population will not change, generation after generation (given our assumptions) • Conclusion 2: if the allele frequencies in a population are given by p and q, the genotype frequencies will be given by p2, 2pq, and q2

  39. Hardy-Weinberg Equilibrium Principle • Why do we use Hardy-Weinberg Equilibrium Principle? • Shows evolution is not happenning • Gives specific set of testable assumptions • If an assumption is violated, the Conclusions do not hold • Is a null model with which to test for evolution!!!!

  40. Hardy-WeinbergASSUMPTIONS Assumptions of Hardy-Weinberg • There is no selection • All members contribute equally to gene pool • There is no mutation • No new alleles are created • There is no migration • All alleles stay in gene pool • There is a large population size • No random events = genetic drift • Panmixia • Mates are chosen randomly

  41. The Hardy-Weinberg principle • Given certain assumptions, whatever the initial genotype frequencies for two autosomal alleles may be, after one generation of random mating, the genotype frequencies will be p2:2pq:q2, and both these genotype frequencies and the allele frequencies will remain constant in succeeding generations.

  42. The Math • N = total number of individuals • n1 = number of A1A1 individuals • n2 = number of A1A2 individuals • n3 = number of A2A2 individuals • p = frequency of the first allele • q = frequency of the second allele

  43. q = frequency of the second allele The Math • p = frequency of the first allele p + q = 1 always in a two allele system

  44. The Basic Symbols and their Meaning • x = f(A1A1) = n1 / N • y = f(A1A2) = n2 / N • z = f(A2A2) = n3 / N • p = x + ½ y • q = z + ½ y • Back door method: • q = √q2 = √z • Only works if the population is in H-W equilibrium

  45. Why is it so? • p + q = 1 • (p + q)2 = 12 • p2 + 2pq + q2 = 1 • p2 = f(AA) • pq + pq = 2pq = f(Aa) • q2 = f(aa)

  46. Three alleles • p = f(A1) • q = f(A2) • r = f(A3) • p + q + r = 1 • (p + q + r)2 = 12 • p2 +2pq + q2 + 2pr + 2qr + r2 = 1 • f(A1A1) + f(A1A2) + f(A2A2) + f(A1A3) + f(A2A3) + f(A3A3) = 1

  47. What’s it good for? • Predicting genotype frequencies given allele frequencies • Genotypes will approximate a binomial distribution – (p + q)2 = 1 – after 1 generation of random mating. • If we know the allele frequencies in generation 1, we can predict the genotype frequencies in generation 2. • Allele and genotype frequencies will not change as long as the assumptions are met.

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