1. Exam 1 Review September 21, 2015

2. Logistics u3306 LSB at 6:30 on Wednesday, September 23 uClosed book, notes, internet uComputers and software will be available uMix of multiple choice, short answer, and calculations u120 points uCovers everything up to Friday lecture (except Genetic Drift)

3. Foundations of Population Genetics uFamiliarize yourself with Mendel, Lamarck, and Darwin uKnow Mendel’s laws and basics of Mendelian segregation uKnow major types of molecular markers and their strengths and weaknesses uDominant versus codominant markers uProbability calculations

4. Hardy-Weinberg uGenotype and allele frequency calculations uStandard errors uHardy-Weinberg assumptions uCalculations for detecting departure from HW, including biological interpretations! uCalculating allele frequencies for dominant loci

5. Important Points about Inbreeding uInbreeding affects ALL LOCI in genome uInbreeding results in a REDUCTION OF HETEROZYGOSITY in the population uInbreeding BY ITSELF changes only genotype frequencies, NOT ALLELE FREQUENCIES and therefore has NO EFFECT on overall genetic diversity within populations uInbreeding equilibrium occurs when there is a balance between the creation (through outcrossing) and loss of heterozygotes in each generation

6. Fixation Index uThe difference between observed and expected heterozygosity is a convenient measure of departures from Hardy-Weinberg Equilibrium Where H O is observed heterozygosity and H E is expected heterozygosity (2pq under Hardy-Weinberg Equilibrium)

7. Estimating Inbreeding from Pedigrees uMost accurate estimate of f derived from direct assessment of relationships among ancestors Half First-Cousins CA: Common Ancestor

8. Chain Counting uCount links to Common Ancestor starting with one parent of inbred individual and continuing down to other parent  D-B-CA-C-E  N=5 links For multiple common ancestors, m: If common ancestors are inbred as well: Where f CAi is inbreeding coefficient of common ancestor i

9. Inbreeding and allele frequency uInbreeding alone does not alter allele frequencies uYet in real populations, frequencies DO change when inbreeding occurs uWhat causes allele frequency change? uWhy do so many adaptations exist to avoid inbreeding?

10. Mechanisms of Inbreeding Depression uTwo major hypotheses: Partial Dominance and Overdominance uPartial Dominance (really a misnomer)  Inbreeding depression is due to exposure of recessive deleterious alleles uOverdominance  Inherent advantage of heterozygosity  Enhanced fitness of heterozygote due to pleiotropy (one gene affects multiple traits): differentiation of allele functions  Bypass homeostasis/regulation

11. Heterozygous Effect h = 0, A 1 dominant, A 2 recessive h = 1, A 2 dominant, A 1 recessive 0 < h < 1, incomplete dominance h = 0.5, additivity h < 0, overdominance h > 1, underdominance A 1 A 1 A 1 A 2 A 2 A 2 Relative Fitness (ω)ω 11 ω 12 ω 22 Relative Fitness (hs)1 1-hs 1-s

12. Putting it all together A 1 A 1 A 1 A 2 A 2 A 2 Relative Fitness (ω)ω 11 ω 12 ω 22 Relative Fitness (hs)1 1-hs 1-s Δq =pq[q(ω 22 – ω 12 ) - p(ω 11 - ω 12 )] ω Reduces to: Δq =-pqs[ph + q(1-h)] 1-2pqhs-q 2 s

13. Modes of Selection on Single Loci uDirectional – One homozygous genotype has the highest fitness  Purifying selection AND Darwinian/positive/adaptive selection  Depends on your perspective!  0 ≤ h ≤ 1 uOverdominance – Heterozygous genotype has the highest fitness (balancing selection) h 1 uUnderdominance – The heterozygous genotypes has the lowest fitness (diversifying selection) h>1, (1-hs) 0 ω A1A1A1A1 A1A2A1A2 A2A2A2A2 ω A1A1A1A1 A1A2A1A2 A2A2A2A2 ω A1A1A1A1 A1A2A1A2 A2A2A2A2

14. Equilibrium under Overdominance uAllele frequency always approaches same value of q when perturbed away from equilibrium value uStable equilibrium uAllele frequency change moves population toward maximum average fitness

15. Equilibrium under Underdominance uAllele frequency moves away from equilibrium point and to extremes when perturbed uUnstable equilibrium uEquilibrium point is at local minimum for average fitness uPopulation approaches trivial equilibria: fixation of one allele

16. Important Points about Selection uDirectional selection usually affects individual loci uDirectional selection removes diversity and reduces genetic variance uOverdominance and underdominance can help maintain diversity in a population under certain conditions uEven in a finite population, diversity can be maintained by antagonistic pleiotropy, spatial and temporal variation in selection, frequency- dependent selection, and coevolution