1. Lecture 11: Genetic Drift and Effective Population Size October 1, 2012

2. Last Time uIntroduction to genetic drift uFisher-Wright model of genetic drift uDiffusion model of drift uEffects within and among subpopulations

3. Simple Model of Genetic Drift uMany independent subpopulations uSubpopulations are of constant size uRandom mating within subpopulations N=16

4. Effects of Drift uWithin subpopulations  Changes allele frequencies  Degrades diversity  Reduces variance  Does not cause deviations from HWE uAmong subpopulations (if there are many)  Does NOT change allele frequencies  Does NOT degrade diversity  Increases variance in allele frequencies  Causes a deficiency of heterozygotes compared to Hardy- Weinberg expectations (if the existence of subpopulations is ignored) (to be covered in more detail later)

5. Today uInteractions of drift and selection uEffective population size uExams!

6. Effects of Drift Simulation of 4 subpopulations with 20 individuals, 2 alleles uRandom changes through time uFixation or loss of alleles uLittle change in mean frequency uIncreased variance among subpopulations

7. Example: Drift and Flour Beetle Color uTribolium castaneum experiment with lab populations of different sizes uFrequency of body color polymorphisms: single locus, black, red, brown uWhy does frequency of wild-type allele increase over time? uWhy does this depend on population size? Conner and Hartl 2004 N=10 N=20 N=50 N=100

8. Effects of Selection on Allele Frequency Distributions No Selection N=20 s=0.1, h=0.5 uSelection pushes A 1 toward fixation uA 2 still becomes fixed by chance 3.1% of the time

9. Genetic drift versus directional selection s=0.1,h=0.5, p 0 =0.5 uDrift eventually leads to fixation and loss of alleles uDrift and selection combined push fit alleles to fixation more quickly than drift or selection alone uSome “unfit” alleles do become fixed uWhat happens without drift?  No populations are fixed for A1 after 20 generations  How long until these become fixed?

10. uDrift can counter selection in very small populations uProblem 4 in Wednesday’s lab exercise contrasts two cases that fall on the middle curve N=10, s=0.25 N=100, s=0.25 Fixation as a Function of Ns and Starting Allele Frequency

11. Combined Effects of Drift and Selection uProbability of fixation of a favorable allele will be a function of initial allele frequency, selection coefficient, heterozygous effect, and population size uFavorable alleles won’t necessarily go to fixation when drift is involved uDrift reduces efficiency of selection in the sense that unfavorable alleles may not be purged from population uFavorable alleles do increase in frequency more quickly when drift is involved over ALL subpopulations uCan be simulated by allowing selection to alter allele frequencies prior to effects of drift

12. Nuclear Genome Size uSize of nuclear genomes varies tremendously among organisms: C-value paradox uNo association with organismal complexity, number of chromosomes, or number of genes Arabidopsis thaliana 120 Mbp Poplar460 Mbp Rice 450 Mbp Maize 2,500 Mbp Barley5,000 Mbp Hexaploid wheat16,000 Mbp Fritillaria (lilly family) >87,000 Mbp

13. Noncoding DNA is part of Answer Fugu: 365 Mbp Human: 3500 Mbp

15. opossum ~ 52% rice ~ 35% Arabidopsis ~ 14% Drosophila ~ 15% pufferfish ~ 2% barley ~ 55% wheat ~ 80% corn ~ 70% Human ~ 45% mouse ~ 40%

16. Why is there so much variation in genome size? Why do microbes have so much simpler genomes than eukaryotes? Why do trees have such huge genomes?

17. The importance of Genetic Drift and Selection in Determining Genome Size uLarge effective population sizes mean selection more effective at wiping out variations with even minor effects on fitness uTransposable elements and introns eliminated from finely-tuned populations, persist where drift can overwhelm selection Lynch and Conery 2004 Science 302:1401

18. Historical View on Drift uFisher  Importance of selection in determining variation  Selection should quickly homogenize populations (Classical view)  Genetic drift is noise that obscures effects of selection uWright  Focused more on processes of genetic drift and gene flow  Argued that diversity was likely to be quite high (Balance view) uControversy raged until advent of molecular markers showed diversity was quite high uNeutral theory revived controversy almost immediately

19. Effective Population Size uCensus population size often inappropriate for population genetics calculations  Breeding population size often smaller uFor genetic drift, historical events or nonrandom mating patterns might reduce EFFECTIVE size of the population uEffective Population Size is an ideal population of size N in which all parents have an equal probability of being the parents of any individual progeny. also uThe size of a theoretically ideal population that would have the same observed level of genetic drift

20. Factors Reducing Effective Population Size uUnequal number of breeding males and females uUnequal reproductive success uChanges in population size through time  Bottlenecks  Founder Effects

21. Table courtesy of K. Ritland Effective Population Size: Effects of Different Numbers of Males and Females See Hedrick (2011) page 213 for derivation

22. Effect of Proportion of Males in the Population on Effective Population Size

23. uSmall population size in one generation can cause drastic reduction in diversity for many future generations uEffect is approximated by harmonic mean Variation of population size in different generations See Hedrick (2011) page 219 for derivation

24. Effective Population Size: The bottleneck effect “Alleles” in original population “Alleles” remaining after bottleneck

25. The Founder effect uOutlying populations founded by a small number of individuals from source population uAnalogous to bottleneck uExpect higher drift, lower diversity in outlying populations

26. Exam Issues uGenotype frequency versus allele frequency (problem 2A, 7) uMeaning of the chi-square: larger than critical value, reject null hypothesis uRecessive alleles and fitness (Multiple choice problem 3; problem 5)