1. Mendelian Genetics in Populations II: Migration, Genetic Drift, and Nonrandom Mating • Motivation • What happens when we depart from HW assumptions? • Pattern of genetic diversity, fitness consequences.

2. II. Migration Also among islands, or between populations on the mainland, etc.

4. Effect of migration on allele frequencies: m, 1-m, p and pm p’ = p after migration p’ = p(1-m) + pm(m) Change in p = p’ – p = p(1-m) + pm(m) – p = = p – pm + pm(m) – p = m(pm – p) Effect is to homogenize!

5. Variation in allele frequencies among populations of red bladder campion Silene dioica

6. Silene dioica on Skeppsvik Archipelago, Sweden

7. Fst = (He – Ho)/ He

8. Migration and selection in banded water snakes

9. Banded (A1A1, A1A2 ) is dominant to unbanded (A2A2)

10. Variation in color pattern within and between populations A = Unbanded, D = Banded, B and C = Intermediate

11. The combined effects of selection and migration on allele frequencies in island water snakes ~ equilibrium

12. III. Drift and Consequences for Genetic Diversity

13. Coin Toss

15. The founder effect in an island-hopping bird silvereye, Zosteropslateralis.

16. Silvereyes have been documented to colonize new islands in recent history.

17. Allelic diversity has declined along the silvereye's route of travel

18. Allelic diversity in the Pacific Field Cricket

19. High frequency of disease alleles in small populations: Pingelapese, Quebecois, Ashkenazy, Lancaster Dutch, etc.

20. Simulations of genetic drift in populations of different sizes

21. Effect of sampling variation after many generations Change in allele frequencey of Drosophila melanogaster populations

23. Effective population size: The size of the population that would give rise to the observed loss of heterozygosity each generation, or increase of variation between populations each generation. Variation in sex ratios: Ne = (4NmNf)/(Nm + Nf) (Genghis Kahn example) Imagine 10,000 males and 10,000 females all reproducing then Ne = 20,000 Vs 1 male and 10,000 females = (40,000)/10,001 = 4

24. Ne = harmonic mean number of individuals across generations: H = N/(1/x1 + 1/x2, + …1/xn) Imagine the following population dynamics: A population is founded by 10 individuals and then grows by 10X each generation for 10 generations: 10, 100, 1000, ….1010 Ne = 10 (generations)/(1/10 +1/100 +1/1000...1/100,000,000,000) Ne = 10/0.1111111111 Ne ~ 90 individuals!!!! Once a population is inbred, the inbreeding is NEVER LOST

25. Heterozygosity decreases by 1/2Ne per generation Example: Imagine a population of 3 zygotes: A1A2 A3A4 A5A6 producing A1, A2, A3, A4, A5, and A6 gametes The chance is 1/6 that any of the next generation zygotes will be homozygous

26. Consequences of Fragmentation Wahlund Effect: All of the same consequences as Drift decreases heterozygosity within populations increases homozygosity within populations increases genetic relatedness within populations

28. Random mating??

30. Drift and Rates of Evolutionary Change

33. Clock like substitution rate Drift??

35. Why are substitution rates uniform across species with different generation times??

40. Codon bias correlates with the relative frequencies of tRNA species

43. IV. Dynamic Interplay between Drift and Selection

44. Selection is only effective if its strong or acting in a large population Deleterious Neutral Beneficial

45. Selection of D. melanogaster for resistance to ethanol fumes in Large vs. Small populations Weber, 1992 L = Large S = Small Resistance (minutes) Generation Consider response to global climate change!

46. Roughly 1- 10% of all sequence difference due to selection or 90 – 99% due to drift

47. V. Inbreeding • Drift can lead to inbreeding • Drift and inbreeding can have the same consequences

48. Leviticus Chapter 18 1 And HaShem spoke unto Moses, saying: 2 Speak unto the children of Israel, and say unto them: I am HaShem your G-d. 3 After the doings of the land of Egypt, wherein ye dwelt, shall ye not do; and after the doings of the land of Canaan, whither I bring you, shall ye not do; neither shall ye walk in their statutes. 4 Mine ordinances shall ye do, and My statutes shall ye keep, to walk therein: I am HaShem your G-d. 5 Ye shall therefore keep My statutes, and Mine ordinances, which if a man do, he shall live by them: I am HaShem. 6 None of you shall approach to any that is near of kin to him, to uncover their nakedness. I am HaShem. 7 The nakedness of thy father, and the nakedness of thy mother, shalt thou not uncover: she is thy mother; thou shalt not uncover her nakedness. = Parent-Offspring, MUTATION (1/4) 8 The nakedness of thy father's wife shalt thou not uncover: it is thy father's nakedness. FAMILY DYNAMICS 9 The nakedness of thy sister, the daughter of thy father, or the daughter of thy mother, whether born at home, or born abroad, even their nakedness thou shalt not uncover. = Full/half sib MUTATION (1/4, 1/8) 10 The nakedness of thy son's daughter, or of thy daughter's daughter, even their nakedness thou shalt not uncover; for theirs is thine own nakedness. = Grandparent-Grandchild, MUTATION (1/8) 11 The nakedness of thy father's wife's daughter, begotten of thy father, she is thy sister, thou shalt not uncover her nakedness. = half sib, MUTATION (1/8) 12 Thou shalt not uncover the nakedness of thy father's sister: she is thy father's near kinswoman. = Aunt-nephew, MUTATION (1/8) 13 Thou shalt not uncover the nakedness of thy mother's sister; for she is thy mother's near kinswoman. = Aunt-Nephew MUTATION (1/8) 14 Thou shalt not uncover the nakedness of thy fathers brother (niece-uncle) MUTATION (1/8), thou shalt not approach to his wife she is thine aunt (nephew-unrelated aunt). 15 Thou shalt not uncover the nakedness of thy daughter-in-law: she is thy son' wife; thou shalt not uncover her nakedness. FAMILY DYNAMICS 16 Thou shalt not uncover the nakedness of thy brother's wife: it is thy brother's nakedness. FAMILY DYNAMICS

49. Torah: Prohibited Matings And Allowable Matings Prohibited: 7: Parent-Offspring (Genetic: probability of 2 copies of same mutation = 1/4) 8: Stepmother-Offspring 9: Full-sib (both parents in common) (Genetic: 1/4) and half-sib (one parent in common) (Genetic: 1/8) 10: Grandfather-Granddaughter (Genetic: 1/8) 11: Half-sib (through father) (Genetic: 1/8) 12: Aunt (father’s side)-Nephew (Genetic: 1/8) 13: Aunt (mother’s side)-Nephew (Genetic: 1/8) 14: Uncle (father’s side)-Niece (Genetic: 1/8), Nephew-Aunt (unrelated) 15: Father-Daughter-in-law 16: Brother-Sister-in-law Allowable: Grandmother-Grandson (1/8), Mother-Son-in-law, Uncle (mother’s side)-Niece (1/8) First Cousin = 1/16

50. Modern Views of Inbreeding(mating among relatives)