Biology 331 Genetics

1. Biology 331 Genetics Population Genetics (Microevolution)

2. Introduction to Evolution: • Population Genetics (Microevolution): • Evolution occurring at and below the species level • Macroevolution: • Evolution occurring at and above the species level • Outgrowth of agricultural revolution in the 20's-40's

3. Modern importance of population genetics: • Agriculture • Other genetic engineering • Forensics • Medicine • Conservation • "Pure" Science • speciation, systematics, evolution of behaviors etc.

4. Variation • Qualitative • Quantitative

5. Evolution: • What is it? • Means Change • Biological/Organic Evolution Change in an organism over time • Change in allele frequency over time • Not = Natural Selection

6. Natural Selection: How does it work? • More offspring are produced than can survive (Species could reproduce at an exponential rate) • Most populations have a stable size • Therefore: There is a struggle for existence • Members of a population vary in their characteristics • (short, tall, fast, slow) • Much of this variation is heritable • Therefore: Struggle for existence is not random. It depends on individual characteristics • (which are heritable)

7. Natural Selection Continued • Those which are best adapted to the environment survive and reproduce (Differential Reproduction) • Over time this process brings about changes in populations with favorable changes accumulating. • Examples: • Cheetah's Speed, Cow's Milk etc. • Fitness: • The ability of an organism to leave offspring in a given environment • Genetics: • Darwin lacked a method. Mechanism provided by the monk Gregor Mendel. 1932-1953 modern synthesis

8. Pepper Moth

9. Items of note: • Selection on individuals, but individuals do not evolve, populations do • Natural selection acts on phenotypes but evolution is change in gene frequency • Natural selection does not "think ahead". Selects organisms adapted to past environments. But, some traits may be • favorable in new environments • human bipedalism • Natural Selection acts only on existing traits, variation is crucial • Natural selection results in organisms better adapted for an environment...NOT optimally designed • human bipedalism • Natural selection normally acts on individuals not groups/species.

10. Hardy-Weinberg: An introduction

11. Hardy-Weinberg Theorem: • Allele frequencies stay constant if there is no selection and it's other assumptions are met • Thus if we have 25% green eye genes, 25% blue eye genes, and 50% brown eye genes it will stay that way. • Heterozygosity will also stay the same

12. Two allele equation: • p2 + 2pq + q2 = 1 • p= frequency of allele A • q = Frequency of allele a • p + q = 1. • So p2 = AA, q2 = aa, and pq = Aa

13. Sophisticated Punnet square:

14. Genotype frequency

15. Assumptions: • Random mating • Very large Population size • Diploid • Sexual • Non-overlapping generations • No migration • No mutation • No selection.

16. So what good is it? • Provides an evolutionary baseline • Calculate deviations from the H.W. Ideal

17. Hardy-Weinberg and Selection: • Problem #1 • Assume a population has two co-dominant alleles for a gene (B, B') • Assume there are 1000 individuals, 250BB, 500BB', and 250B'B' • So: Freq. B = 500+500/2000 = .5; B'= 500+500/1000 = .5 • Assuming H.W. BB = p2 = .25; BB'= 2pq = .5; B'B'= q2 = .25 (No Change)

18. Add Selection: • Fitness = Survival (for this example) • BB = 1; BB'= 0.9, B'B'= 0.8 • BB = 250; BB'= 0.9(500) = 450; B'B'= 0.8(250) =200 • Frequency BB = 250/900 = .278; BB'= 450/900 = 0.5; B'B'= 200/900 = .222 • Frequency B = .278+1/2(.5) = .528, B' = .472 • Deviation From H.W.!

19. Types of selection

20. Frequency dependant selection • Fitness of an allele depends upon its frequency

21. Mutation and Hardy Weinberg: • Assume p has a frequency of 1 • What is the frequency of q ? • Now allow a mutation to occur from p to q • Instant evolution! • But is this a "strong" evolutionary effect? • Highest rate of mutation recorded is 0.0007/mutant cells/cell division • Result....no real effect over one generation • Over time? • Mutation alone is typically a weak evolutionary force

22. Mutation over time

23. So why does in matter? • Raw material for evolution • Creates new genes • Mutation selection balance

24. Migration: Transfer of alleles from one gene pool to another

25. One island model: • Assume you have genotypes A1A1, A1A2, A2A2 • frequencies p2, 2pq, and q2 • A1 is fixed on the continent; A2 is fixed on the island • N on the island is much smaller than on the continent • Migration (m) from the continent to the island is more important than vice versa (Why?) • m=20% of the island population/generation • A1A1 = 0.2 after migration (was 0) • A2A2 = 0.8 after migration (was 1.0) • Not H.W. equilibrium • Both allele frequencies and genotype frequencies changed

26. Islands

27. Long term effect?? • The general effect of migration is homogenization • This effect is proportional to m, and the difference between Pc and PI • Migration selection balance • Migration as mutation

28. Gene flow and natural selection

29. Genetic Drift: • Random variation in allele frequencies due to sampling error • Yields evolution but not necessarily adaptation • Drift more important in small populations • Coin flipping/beanbag examples

31. Drift

32. Absorbing States: • The random fixation of alleles • The frequencies of alleles vary through time • Eventually alleles go to either fixation or loss • Assumes no Migration, mutation, selection etc. • Probability of loss or fixation proportional to initial frequency • "C" allele example

33. Loss and Fixation

34. Drift

35. What determines probability of loss? Probability of loss or fixation proportional to initial frequency So why does population size matter? "C" allele example

36. Speed

37. Bottle Necks: • "Random" reduction in population size (Disasters) • Only a fraction of the alleles in the initial population survive • "Instant" Evolution (sampling error) • Small population size after the bottleneck enhances drift • Repeated bottlenecks have huge effect! • European Jews, Lynx, Whales • S. African Cheetahs and Northern Elephant seals almost "Clones"

38. Bottlenecks

39. Bottlenecks • "Instant" Evolution (sampling error) • Small population size after the bottleneck enhances drift • Repeated bottlenecks have huge effect! • European Jews, Lynx, Whales • S. African Cheetahs and Northern Elephant seals almost "Clones"

40. Founder Effect: • Genetic drift in a new colony • May be only one gravid female • Sampling error can result in "instant" evolution • Very much like a bottleneck • Extreme sampling error possible

41. Founder Effect

42. Picture Wing Drosophila

43. Examples • Tristan da Cunha (Classic Example) • Founded by a small number of colonists (15) • Retinitis Pigmentosa (one founder was a carrier) • Amish in PA • Founded by 200 people • 1-2 founders have Ellis-van Creveldsyndrom • Frequency 0.07 in Amish, 0.001 in the population as a whole

44. Village of Salinas:In the remote mountains of the Dominican Republic:

45. One village founder Altagracia Carrasco • Several children with at least 4 women • Large contribution to a small population

46. Mutant for 5-alpha reductase-2 gene • Low catalytic activity • He was a heterozygote • Enzyme responsible for conversion of testosterone to DHT • Required for full masculinization of external genitalia • Results in XY “females”

47. What happens at puberty? • Guevedoces (penis at twelve)

48. Effective Population Size: • Theoretical "ideal" population having the same magnitude of drift as the "Real"(tm) population • Census size: • All the individuals in a population • Assume No selection, No migration, No mutation, Non overlapping generations, Diploid, Sexual • No population obeys the rules so we need a "fudge factor" • Effective population size almost always smaller than the census size

49. Example: • Assume 500 individuals • 250 breeding age • Only 5 "dominant" males breed • EPS = 130

50. Drift and selection: • Can allow selection to act • "C" allele again!