1. Adaptation What is Adaptation? Not Phenotypic Plasticity Not Genetic Drift Must be targets of selection (not Pleiotropy, not linkage)

2. What is Adaptation? Genetic change in a population resulting from natural selection, whereby the average state of a character becomes improved with respect to a specific function, allowing an organism to achieve greater fitness in its environment.

3. Evolution is the change in allele frequency at each generation in a population One way in which evolution occurs is through Natural Selection Darwin (1809-1882)

4. Darwin’s Contribution: Natural Selection “Of course, long before you mature, most of you will be eaten” Too many offspring are produced Limited resources and competition Variation in a population Better adapted individuals survive Survivors leave more offspring (“fitness) Thus, the average composition of the population is altered Natural selection leads to adaptation

5. “Population speciation through Natural Selection”

6. Mutation

7. This mutation happens to be beneficial

8. Individuals with this mutation happen to leave more offspring (greater “fitness”)

9. Requires Natural Selection Requires heritable variation (polymorphism) in a population MUST have an effect on Fitness there is some selective force Is a allele frequency change in a population Adaptation

10. Critique of the “Adaptationist Programme” (2) Critique of the “Adaptationist Programme” Gould & Lewontin 1979 One of the most important papers in Evolutionary Biology They critique the “Adaptationist” and “Panglossian Programme” that assumes that a phenotypic change is the result of adaptation Gould & Lewontin point out tha t not all phenotypic variation or phenotypic evolution is the result of adaptation

11. Gould & Lewontin: The spandrels of San Marco San Marco Cathedral, Venice

12. Gould & Lewontin: The spandrels of San Marco might not have been created for a reason, but might simply be a byproduct due to the creation of arches San Marco Cathedral, Venice

13. Gould & Lewontin Other potential causes of phenotypic variation that is NOT Adaptation: (A) Plasticity: phenotypic change without evolution (B) Nonadaptive Evolutionary Forces: Genetic Drift Genetic Constraint (Linkage, Pleiotropy) (C) Physical Constraint (allometry, mechanically forced correlation)

14. Outline (1) What is Adaptation? Not Phenotypic Plasticity Not Genetic Drift Must be targets of selection (not Pleiotropy, not linkage)

15. AdaptationvsPlasticity

16. Definition - Plasticity Differences in phenotype that a genotype exhibits across a range of environments Some traits with a plastic component: height, temperature tolerance, salinity tolerance, muscle mass…

17. Acclima(tiza)tion (≠ Adaptation) 1) Result of Phenotypic Plasticity 2) Not heritable 3) Short term or developmental response within a single generation 4) Arises through differential gene expression or other regulatory mechanism rather than natural selection

18. Types of Plasticity Short-term reversible Development acclimation: generally irreversible Genotype --> Development --> Phenotype Within normal tolerance range In response to Stress

19. Dodson, SI. 1989. Predator induced reaction norms. BioScience 39:447–452 Developmental plasticity

20. Hebert and Grewe, 1985 Predator induced formation of helmets in Daphnia

21. Plasticity can be depicted graphically as a Reaction Norm Response Environment Reaction Norm : the function which describes the plastic response

22. Reaction Norms P= G + E V P =V G +V E

23. In the case of plasticity, the different phenotypes in different environments are NOT the result of Adaptation… The Genotype(s) in the environments are NOT changing The differences between them are due to differences in response (such as gene expression) in different environments Response Environment

24. Most Importantly, Must distinguish plasticity from adaptations to understand heritable (and permanent) vs inducible differences, in order to interpret experiments properly

25. How control for plasticity in Experiments? If you want to determine whether a trait is the result of plasticity or genetically based, you need to perform a common- garden experiment to remove the effects of environmental plasticity.

26. What is a common-garden Experiment? An Experiment in which individuals from different populations or species are reared under identical conditions (can be over a range of conditions) Remove differences due to environmental plasticity

27. Different Populations Rear under common conditions To determine the differences when the environment is held constant Common Garden Experiment

28. Different Populations If the populations still differ under common-garden conditions, the differences are genetically based. But are these genetic differences the result of adaptation? Common Garden Experiment

29. Outline (1) What is Adaptation? Not Phenotypic Plasticity Not Genetic Drift Must be targets of selection (not Pleiotropy, not linkage) Lecture 2: genetic mechanisms of adaptation how to detect and analyze adaptation

30. Genetic Drift Definition: Changes in allele frequency from one generation to the next simply due to chance (sampling error) The change in genetic composition (evolution) depends on Who leaves Offspring, the # of Offspring, and Which Offspring happen to survive (which gametes, which alleles)

31. Genetic drift N = 100 p A = 0.5 T = 100 generations Futuyma (2009)

32. Outline (1) What is Adaptation? Not Phenotypic Plasticity Not Genetic Drift Must be targets of selection (not Pleiotropy, not linkage) Lecture 2: genetic mechanisms of adaptation how to detect and analyze adaptation

33. Linkage Phenotypic evolution could arise due to linkage (≠adaptation): Genes might experience an evolutionary shift because another gene closely linked on the chromosome is under selection (selective sweep) This is a genetic mechanism of change that is NOT adaptive Definition: The tendency for certain alleles to be inherited together due to their physical proximity on the chromosome Human linkage map

34. Linkage Consequence: Selection at a locus (gene) might cause selection at many other genes closely linked on a chromosome, even if there is no reason for those other genes to evolve Definition: The tendency for certain alleles to be inherited together due to their physical proximity on the chromosome Human linkage map

35. Linkage “Selection toy” Selection for ball size or for ball color? (After Futuyma 2009, Sober 1984)

36. Pleiotropy Definition: The phenomenon where a gene affects several different traits If a gene controls the expression of many traits, selection at that gene will affect those many traits Consequence: selection at a gene due to the importance of evolution of one trait could affect many other traits that are affected by that gene

37. Physical Constraint Developmental constraint Constraint in Body Plan If body size increases, brain size has to increase If a larger eye evolves, need a bigger socket (the socket itself is not the target of selection) Analogy: the Spandrels of San Marco

38. Gould & Lewontin on Physical Constraint: The spandrels of San Marco might not have been created for a reason, but might simply be a by product due to the creation of arches San Marco Cathedral, Venice

39. Adaptations are ubiquitous, but demonstrating that a particular trait is an adaptation is not always easy

40. How can you tell if a trait evolved as a result of adaptation? (1) The trait must be heritable The differences between populations are genetically based differences rather than inducible differences (plasticity) (2) The trait has fitness consequences (promotes survival, performance, and number of offspring) (If a trait evolved due to genetic drift, linkage or pleiotropy it may confer no fitness advantage)

41. How do we detect Evolutionary Adaptations? Transgenic and gene knockout studies Is that gene causing the trait, and does it have fitness consequences? That’s why we use mice to understand human genetics

42. Examples: Adaptation or not? After high altitude training athletes have increased number of red blood cells (RBC) Tibetans and Sherpas have higher RBC than lowland (<2000 m) people (Yi et al. 2010, Science 329:75-78)

43. Weeds in a cornfield have been found to grow taller than those in soybean fields when both populations are reared in common-garden conditions Taller weeds in the cornfields survive at a greater rate and leave more offspring Examples: Adaptation or not?

44. EPIGENETICS

45. WHAT IS EPIGENETICS? Epigenetics – gene regulation changes that does not involve a change in DNA sequence INHERITEDEpigenetic changes can be INHERITED!!

46. Common mechanisms may include but not limited to: - DNA methylation - Histone modifications (De) Acetylation (De)Methyaltion, Ubiquitination, Phosphorylation -Regulatory non-coding RNAs EPIGENETICS

47. DNA methylation