1. Genetic Linkage

3. Two pops may have the same allele frequencies but different chromosome frequencies.

4. Conditions for Linkage Equilibrium (Two locus case) 1)Frequency of B is the same on chromosome A and a 2)Frequency of haplotypes AB, ab, Ab, aB can be calculated from allele frequencies A=p, a=q, B=t, and b=s. f(AB) = pt f(ab) = qs f(Ab) = ps f(aB) = pt 3) Coefficient of linkage disequilibrium (D) = 0 f(AB) x f(ab) - f(Ab) x f(aB) = D ps x qt - pt x qs = 0 (ranges from -0.25 to +0.25)

5. Hardy Weinberg Principle for Two Loci Chromosome frequencies remain unchanged across generations if loci are in linkage equilibria. If loci are in linkage disequilibria, the chromosome frequencies will move closer to linkage equilibrium each generation. What Creates Linkage Disequilibrium in a Population? selection, drift, and population admixture

6. Effects of Selection on Chromosome Frequencies ab/ab = body size of value 10 each additional A or B adds 1 value predators eat all individuals of size 12 or less 65.28% survive

7. 65.28% survive Freq a = (0.1536 + 0.1536) /.6528)/2 = 0.24 Freq b = (0.0576 + 0.0576) /.6528)/2 = 0.09 Freq ab =.24 x.09 =.02 however! Locus A and B are in disequilibrium among the survivors

8. Genetic Drift, followed by selection can cause linkage disequilibrium

9. Admixture Combination of Two Different Gene Pools

10. Recombination Breaks Down Linkage Disequilibria The rate of decline in LD increases with r

11. LD declines over time (rate depending on r) r = D sqrt(pqst)

13. Concept of Linkage a A B b Meiosis Law of Independent Assortment ABAB AbAb aBaB abab = 0.25 All allele combinations in gametes equally probable Aa Bb Meiosis Probability of recombination = 0.5 ABAB AbAb aBaB abab = 0.25 All allele combinations in gametes equally probable

14. Aa B b Meiosis Probability of recombination = 0.3 A a B b Meiosis Probability of recombination = 0.1 ABAB AbAb aBaB abab All allele combinations in gametes NOT equally probable = 0.15 = 0.35 ABAB AbAb aBaB abab = 0.05 = 0.45 Linked Loci All allele combinations in gametes NOT equally probable

15. Concept: The closer two loci are on a chromosome, the lower the probability of recombination. Why important? (1) Affects rate that LD is broken down. (2) Allows one to determine the linear order of genes on a chromosome (make a genome map). (3) Maps allow for the localization of genes, mutant phenotypes, and QTL in the genome.

16. Selection has an effect on frequency of B alleles Selection at a single locus affects other loci under LD

17. LD among 1504 marker Loci on Human Chromosome 22. (Dawson et al. 2002)

18. Time (generations) Linkage Disequilibria Decay of LD Present level

19. For neutral alleles: Genetic drift is the primary evolutionary mechanism. So: Indicates alleles at the locus may be under selection. How does LD help identify genes that may be under positive natural selection? If LD is not detectable, indicates that an allele is old. Expect old and frequent alleles, or old and rare alleles, But do not expect young, high frequency alleles. If LD is detectable, indicates that an allele is young. Expect magnitude of LD is proportional to the age of an allele.

20. G6PD polymorphism and deficiency Countries with malaria have highest frequency of a reduced-activity allele.

21. Characterized SNPs for G6PD locus of 230 men Nine different G6PD alleles diagnosed by 11 SNPs Sabeti et al., 2002 Typed each allele for 14 SNPs outside the G6PD locus

22. LD is higher for the G6PD-202A allele; suggests positive selection Probability that 2 randomly chosen “a” chromosomes have the same snps across a physical distance

23. The Evolutionary Biology of Sex KiwiMilk weed aphid There is Amazing Diversity in Reproductive Mode

24. Blueheaded Wrasse

25. Sexual Reproduction Probably Evolved Early In Life Dandelion Taraxacum officinale Bdelloid rotifer Examples of parthenogenesis

26. What Mode of Reproduction is Better? An asexual female will have 2x as many grandchildren!

27. Why Aren’t All Species Asexual? Because asexual populations accumulate deleterious mutations Termed: Muller’s Rachet Possibly leads to extinction

28. None of the 444 cultures had higher fitness than the wild type Evidence for Muller’s Ratchet: Andersson and Hughes (1996)

29. Barrett and Charlesworth, (1991) Eichhornia paniculata

30. Flower number declined in a natural out crossing population, and heterosis was observed. Flower number stayed relatively constant in a naturally self-fertilizing population

31. Recombination Breaks the Ratchet Sex maybe advantageous because it can recreate favorable multilocus genotypes However, adaptation by this process is only faster in large populations

32. However, Suppression of Recombination is Important in the Evolution of Sex Chromosomes

33. Hypotheses for Short-Term Advantages of Sex Recombination allows repair of damaged DNA Genetically diverse progeny may outcompete asexual progeny Muller’s ratchet Deleterious mutations are more easily purged in sexual pops Rate of evolution is higher in large sexual populations