Population Genetics: Understanding Allele Frequencies and Evolutionary Forces, Lecture notes of Biology

Download Population Genetics: Understanding Allele Frequencies and Evolutionary Forces and more Lecture notes Biology in PDF only on Docsity! Population Genetics Reading: B&D sections 7.1-7.3 In-text boxes Required: Box 7.4 Recommended: Boxes 7.1, 7.2, 7.3 Not required: Boxes 7.5, 7.6 Problem Sickle cell anemia is caused by a recessive allele. According to the CDC (https://www.cdc.gov/ncbddd/sicklecell/data.html): • 1 out of every 365 Black or African-Americans is born with the disease • and 1 out of every 13 are carriers What are the frequencies of the sickle cell and healthy alleles in this population? a. Freq(healthy allele) = 0.75, freq(sickle allele) = 0.50 b. Freq(healthy allele) = 0.456, freq(sickle allele) = 0.544 c. Freq(healthy allele) = 0.95885, freq(sickle allele) = 0.04115 d. Freq(healthy allele) = 0.94804, freq(sickle allele) = 0.05196 Population Genetics • Integration of Mendelian genetics into evolutionary theory (recall: Modern Synthesis) • PopGen definition of evolution: ➡ Changes in allele frequencies across generations Any change in the heritable traits within a population across generations Hardy-Weinberg Equilibrium (HWE) • Equilibrium: • “a state of balance between opposing forces or actions” (Merriam-Webster) • HWE is a null model: • “... an ideal state that provides a baseline against which change can be analyzed.” (Wikipedia) Hardy-Weinberg Equilibrium Godfrey Harold Hardy (1877–1947) Wilhelm Weinberg (1862–1937) • What happens to allele frequencies in a population under a simplified set of assumptions? • A null model to understand how alleles are distributed in populations and how allele frequencies change (or not) over time H-W equilibrium Conclusions If these conditions hold, then: 1. Allele frequencies will NOT change. 2. If allele frequencies are p and q, then genotype frequencies are p2, 2pq, and q2. In other words, allele and genotype frequencies will be in equilibrium, and no evolution will occur. Allele frequencies under HWE fr eq f(A) f(a) 1. Allele frequencies will NOT change. Genotype frequencies under HWE 2. If allele frequencies are p and q, then genotype frequencies are p2, 2pq, and q2. Follow to the next generation P(AA) = f(A)*f(A) = p*p = p2 probability that an offspring will have an AA genotype See Box 7.2 for more on probabilities Follow to the next generation P(AA) = f(A)*f(A) = p*p = p2 probability that an offspring will have an AA genotype See Box 7.2 for more on probabilities P(Aa) = [f(A)*f(a)]+[f(a)*f(A)] = (p*q)+(q*p) = 2pq Follow to the next generation P(aa) =f(a)*f(a) = q*q = q2 P(AA) = f(A)*f(A) = p*p = p2 probability that an offspring will have an AA genotype See Box 7.2 for more on probabilities P(Aa) = [f(A)*f(a)]+[f(a)*f(A)] = (p*q)+(q*p) = 2pq Have allele frequencies changed in the offspring? NO! p’=p q’=q At Hardy-Weinberg equilibrium: 1. allele frequencies do not change 2. genotype frequencies: p2, 2pq, q2 H-W equilibrium is NOT p2 + 2pq + q2 = 1 p + q = 1, or These statements are always true, whether a population is in HWE or not Remember: f(A) + f(a) = 1 f(AA) + f(Aa) + f(aa) = 1 Which of the following is true of H-W equilibrium? A. Only when a population is at HWE will p2 + 2pq + q2 = 1 be true. B. In a population at HWE, evolution does not occur. C. Once a population reaches HWE it will always be in HWE regardless of changing environment. D. You can only calculate allele frequencies from genotype frequencies when a population is in HWE. Testing for H-W equilibrium in natural populations AA Aa aa total 3969 3174 927 8070Observed (O) f(A): p = [3969+(3174/2)]/8070 = 0.6885 f(a): q = [927+(3174/2)]/8070 = 0.3115 Abdomen color in Drosophila polymorpha (1949) Testing for H-W equilibrium in natural populations AA Aa aa total (N) 3969 3174 927 8070 p2N 2pqN q2N Observed (O) Expected (E) p = 0.6885 q = 0.3115 Expected number of each genotype, if the population were in HWE Testing for H-W equilibrium in natural populations AA Aa aa total 3969 3174 927 8070 0.474*8070 0.4290*8070 0.0970*8070 Observed (O) Expected (E) p = 0.6885 q = 0.3115 Causes for deviation from H-W equilibrium 1. Selection 2. Mutation 3. Migration 4. Genetic drift 5. Non-random mating Relax the HWE assumption of “no selection” • Individuals do NOT necessarily survive at equal rates and have equal reproductive success. • Differential survival and reproductive success associated with particular alleles • (This should sound familiar from Lecture 3, the conditions for evolution by natural selection...) Fitness and selection coefficients • Recall: Genotype X is fitter than genotype Y if and only if X has a higher probably of survival and/or greater expectation of reproductive success than Y • The selection coefficient, s, describes how much fitter one genotype is than another. • e.g. if genotype Y is only 90% as likely as genotype X to survive, then s = (1.0 - 0.90) = 0.1 relative fitness of X relative fitness of Y (Cavener and Clegg 1981) Results of selection over many generations Effect of dominancepinitial = 0.02 s = 0.5 Recessive Dominant Semi-dominant • A beneficial dominant allele increases in frequency most rapidly when rare. • A beneficial recessive takes longer to increase in frequency, but goes to fixation quickly when common. • A beneficial semi-dominant/incomplete dominant, goes to fixation most rapidly. See Fig. 7.13 Dominance changes the response to selection Effect of dominance: A practical result If a disease is caused by a rare, recessive allele, it will be nearly impossible to eliminate from a population. SCID, Severe Combined Immunodeficiency Heterozygote disadvantage • Aka, underdominance • The heterozygote has a lower fitness than either homozygote • Consequence: One allele will be lost p w AA aa Aa Frequency-dependent selection • The fitness of an allele depends on its frequency in the population • Negative frequency dependent selection: the advantage of rarity • Consequence: maintenance of multiple alleles Frequency-dependent selection scale-eating cichlids left-mouthed right-mouthed (Hori 1993) Practice with simulations Infinite freq A, ——_ | ——_! ——_ |} Reset \1 | {0.996 0.9 0 | [o 0 Freq [0.1 es es EEE ihemaEEEEEEEEEEEEE Change in A, Allele Frequency Over Time 1 0.9 — oe o 08 Op_ ov —— Pop_3 = 07 < Pop_4 gz 06 Pop_5 a 0.5 5 0.4 a g 0.3 u 0.2 0.1 OF T T T T T T T 0 50 100 150 200 250 300 350 Generations http://www.radford.edu/~rsheehy/Gen_flash/popgen/ Things you should know • How to think from the perspective of the population rather than individual • Why HWE is a useful null model • How to apply HWE and test whether a population is in HWE • What the assumptions are for HWE and why they are important • What selection coefficients are and how they impact the response to selection • What directional selection is • What heterozygote advantage and frequency dependent selection are and what there consequences are on evolution Problem 1 In a population of butterflies, blue wing color is determined by a dominant allele (B), green by a recessive allele (G). The frequency of B is 0.3. If the population is in H-W equilibrium, how many green winged butterflies do you expect in a population of 500? a) 255 b) 245 c) 490 d) 0.70 e) 350 f) 150