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Exam 1 Review September 21, 2015 Logistics u 3306 LSB at 6:30 on Wednesday, September 23 u Closed book, notes, internet u Computers and software will be available u Mix of multiple choice, short answer, and calculations u 120 points u Covers everything up to Friday lecture (except Genetic Drift) Foundations of Population Genetics u Familiarize yourself with Mendel, Lamarck, and Darwin u Know Mendel’s laws and basics of Mendelian segregation u Know major types of molecular markers and their strengths and weaknesses u Dominant versus codominant markers u Probability calculations Hardy-Weinberg u Genotype and allele frequency calculations u Standard errors u Hardy-Weinberg assumptions u Calculations for detecting departure from HW, including biological interpretations! u Calculating allele frequencies for dominant loci Important Points about Inbreeding u Inbreeding affects ALL LOCI in genome u Inbreeding results in a REDUCTION OF HETEROZYGOSITY in the population u Inbreeding BY ITSELF changes only genotype frequencies, NOT ALLELE FREQUENCIES and therefore has NO EFFECT on overall genetic diversity within populations u Inbreeding equilibrium occurs when there is a balance between the creation (through outcrossing) and loss of heterozygotes in each generation Fixation Index u The difference between observed and expected heterozygosity is a convenient measure of departures from Hardy-Weinberg Equilibrium H E HO HO F 1 HE HE Where HO is observed heterozygosity and HE is expected heterozygosity (2pq under Hardy-Weinberg Equilibrium) Estimating Inbreeding from Pedigrees u Most accurate estimate of f derived from direct assessment of relationships among ancestors Half First-Cousins CA CA CA CA BB CC DD EE PP CA: Common Ancestor BB CC DD EE PP Chain Counting Count links to Common Ancestor starting with one parent of inbred individual and continuing down to other parent CA A1A2 P(A1) = ½ P(A1) = ½ P(A1) = ½ P(A1) = ½ D E P(A1) = ½ P(A1) = ½ P A1A1 N=5 links N C B D-B-CA-C-E 5 1 1 1 f 2 2 32 For multiple common ancestors, m: Ni 1 f . i 1 2 m If common ancestors are inbred as well: Ni 1 f (1 f CAi ) i 1 2 m Where fCAi is inbreeding coefficient of common ancestor i Inbreeding and allele frequency Inbreeding alone does not alter allele frequencies Yet in real populations, frequencies DO change when inbreeding occurs What causes allele frequency change? Why do so many adaptations exist to avoid inbreeding? Mechanisms of Inbreeding Depression Two major hypotheses: Partial Dominance and Overdominance Partial Dominance (really a misnomer) Inbreeding depression is due to exposure of recessive deleterious alleles Overdominance Inherent advantage of heterozygosity Enhanced fitness of heterozygote due to pleiotropy (one gene affects multiple traits): differentiation of allele functions Bypass homeostasis/regulation Heterozygous Effect A1A1 Relative Fitness (ω) Relative Fitness (hs) ω11 1 h = 0, A1 dominant, A2 recessive h = 1, A2 dominant, A1 recessive 0 < h < 1, incomplete dominance h = 0.5, additivity h < 0, overdominance h > 1, underdominance A1A2 A2A2 ω12 ω22 1-hs 1-s Putting it all together A1A1 Relative Fitness (ω) ω11 Relative Fitness (hs) 1 Δq =pq[q(ω22 – ω12) - p(ω11- ω12)] ω Reduces to: Δq =-pqs[ph + q(1-h)] 1-2pqhs-q2s A1A2 A2A2 ω12 ω22 1-hs 1-s Modes of Selection on Single Loci Directional – One homozygous genotype has the highest fitness Purifying selection AND Darwinian/positive/adaptive selection 1 0.8 ω 0.6 0.4 0.2 0 Depends on your perspective! AAA 1A1 AAa1A2 A2aaA2 AAA 1A1 aa AAa 1A2 A2A2 AAA 1A1 AAa1A2 Aaa 2A2 0 ≤ h ≤ 1 1 Overdominance – Heterozygous genotype has the highest fitness (balancing selection) 0.8 ω Underdominance – The heterozygous h>1, (1-hs) < (1 – s) < 1 for s > 0 0.4 0.2 0 h<0, 1-hs > 1 genotypes has the lowest fitness (diversifying selection) 0.6 1 0.8 ω 0.6 0.4 0.2 0 Equilibrium under Overdominance Allele frequency always approaches same value of q when perturbed away from equilibrium value Stable equilibrium Allele frequency change moves population toward maximum average fitness s1 qeq s1 s2 Equilibrium under Underdominance Allele frequency moves away from equilibrium point and to extremes when perturbed Unstable equilibrium Equilibrium point is at local minimum for average fitness Population approaches trivial equilibria: fixation of one allele Important Points about Selection Directional selection usually affects individual loci Directional selection removes diversity and reduces genetic variance Overdominance and underdominance can help maintain diversity in a population under certain conditions Even in a finite population, diversity can be maintained by antagonistic pleiotropy, spatial and temporal variation in selection, frequencydependent selection, and coevolution