Evolution Lecture 6 : Variation Among Individuals (Chapter 5)

1. Evolution Lecture 6 : Variation Among Individuals(Chapter 5)

2. Variation Genetic variation among individuals in populations is obvious (just look around this room!) But we often overlook variation in other organisms (even though it is often greater)

3. Figure 5-1

4. Variation among individuals is the raw material for evolution by natural selection However, for that to be true, the variation needs to be heritable What are some types of variation that we know are not heritable?

5. Three kinds of variation Genetic- ex. Color of newborns skin varies Environmental-go out in sun and you tan Genotype by environment interactions-depending on genetics, how much you tan varies, even if you spend the same amount of time in the sun

6. Machinery of Life Structure of living things often provided via proteins Proteins also carry out many functions Proteins are chains of amino acids, these amino acids give the protein its form and function

7. Machinery of Life

8. Machinery of Life The “instructions” an oraganims uses to build proteins is in genetic material, DNA (RNA in some viruses) We will focus on DNA

9. Machinery of Life Video on DNA to proteins https://www.youtube.com/watch?v=gG7uCskUOrA Terms to know! Genome Chromosome Nucleotide

10. Machinery of Life The number of chromosomes an organism has is specific to the species The proteins that chromosome codes for is species specific too (what genes the organism has and where they are located on chromosomes)

11. Source of Variation Genetic variation is the result of differences among individuals coded in their DNA (different versions of a protein, quantity produced, etc.) Environmental variation arises when external factors influence the protein production Genotype by environment interaction occurs when individuals have DNA differences that make them react differently to the external factors

12. Human Variation Example Chemical PTC-some people can taste it (very bitter), others cannot Variation in taste receptors taste receptor proteins bind with certain types of flavors TAS2Rs for bitter flavor TASR38 binds to PTC

13. Human Variation Example TASR38 is 333 amino acids long found on chromosome 7 There are 3 places with variation in the amino acids coded for Different versions are called alleles The two common alleles for TASR38 are called AVI and PAV

14. Human Variation Example AVI and PAV alleles You have two chromosome 7’s (one from mom and one from dad) The two chromosomes may carry the same alleles for TASR38 or not The combination of alleles is the genotype, can be PAV/PAV; AVI/AVI; AVI/PAV

15. Figure 5-7

16. Human Variation Example Combination of alleles is the genotype: PAV/PAV; AVI/AVI; AVI/PAV Trait exhibited is the phenotype (what you “see”, here it is what you taste) People with PAV allele often dislike broccoli and similar veggies Balance between avoiding toxins in plants and healthy diet, what genotype?

17. Environmental Variation Water fleas called Daphnia can have morphology that protects it from midges Doubles in thickness of shell, gets ridges, but energetically expensive to make (not worth it if no midges around) Only makes this armor when it smells midge larvae in environment, this is inducible defense

18. Figure 5-8a The Daphnia make more proteins when they smell midges, the proteins are what cause the changes in morphology

19. Environmental Variation Environmental variation is not raw fuel for evolution however, as these changes in phenotype are not passed down genetically, but are altered by the environment the offspring are in

20. Genotype by Environment Interaction Many reptiles have temp. determined sex Leopard geckos develop at cool or hot temps= females, intermediate temps = males Pathway to sex involves different protein production, e.g., timing of Sox9 for gonad development is different between sexes

21. Genotype by Environment Interaction

22. Genotype by Environment Interaction Same father for each “line”, variety of mothers Variation among fathers with degree of how temp affects offspring sex Sensitivity is inherited % male

23. Genotype by Environment Interaction Genetic variation can control the degree to which traits react to differing external factors Phenotypic plasticity-organism develops different phenotypes in different environs Degree of plasticity depends on the genetic variation present in organisms

24. Figure 5-13

25. Where does genetic variation come from? New alleles come from alterations to existing alleles These are mutations-often occur because of errors that occur before/during DNA replication that escape repair

26. Where does genetic variation come from? https://www.youtube.com/watch?v=GieZ3pk9YVo Different types of mutations, all can have major differences Point Transition Transversions Synonymous/Nonsynonymous Nonsense Insertions/Deletions

27. Figure 5-21

28. Where does genetic variation come from? New genes Gene duplication Unequal crossing over Chromosome mutations Genome duplications -Polyploids Can lead to speciation

29. Rates of MutationFitness Can determine mutation accumulation (differences) between lineages for the same genes

30. Figure 5-35

31. Fitness of Mutations Most mutations are not advantageous Some mutations are neutral Lethal and deleterious mutations outnumber beneficial mutations The occasional occurrence of beneficial mutations means populations can increase fitness over time though

32. Fitness over time Lab lines of nematodes where deleterious mutations occur without natural selection decline over time; Natural selection weeds out these lines, allowing the fitter nematodes to thrive

33. Evolution Lecture 7 : Population Genetics: Hardy-Weinberg Equilibrium(Chapter 6)

34. What is population genetics? • Integrates evolution by natural selection with Mendelian genetics • Changes in relative abundance of traits is tied to the relative abundance of alleles that influence them • Evolution here is the change in allele frequencies across generations

35. The Null Model in Population Genetics • We first need to see how allele frequencies operate without selection, migration etc.. • This is a null model...a benchmark at which we can compare changes in real populations due to other factors • What is a population? A group of interbreeding individuals and their offspring

36. How do we determine allele frequencies? • Example: Examine a population of 43 individuals for the CCR5-32 gene • We have a total of 86 alleles • If we have 16 heterozygotes and one homozygote for the - allele, then we get a frequency of this gene at 16+2/86=0.209 • The other (+ allele) is 52+16/86=0.791 • The frequency of both alleles must = 1.0 • We could also do this by: homo +: 26/43=0.605, het: 16/43=0.372, homo -: 1/43=0.023. Therefore the - allele freq. is = 0.023 x 1/2 (0.372)=0.209

37. Generic Life-Cycle: From haploid to diploid. Alleles taken from haploid stage as individual genes are combined into the diploid stage

38. The allele frequency is 0.4 a and 0.6 A

39. By randomly plucking gametes and making zygotes, we see that our frequencies change over time

40. Numerical Calculation • If 60% of Eggs Contain A allele, and 60% Sperm Contain A allele, then we can make predictions about the probability of Zygotes • AA=0.6x0.6=0.36 • Aa=2(0.6x0.4)=0.48 • aa=0.4x0.4=0.16 • These must equal one • If the population is in equilibrium, the frequencies remained the same form generation to generation

41. Figure 6-6

42. Figure 6-7

43. Hardy-Weinberg Equilibrium • Yule thought that equilibrium meant that the allele freq. must be 0.50 and 0.50 • Hardy demonstrated that they don’t have to be 0.50/0.50, but simply must remain the same between generations • If allele freq. are given by p and q, then the genotypes can be calculated by p2+2pq+q2=1 • Also, p+q=1

44. In Order for Equilibrium to be Maintained We Assume • No Selection • No Mutation • No Migration • No chance events • Random mating • So, if allele freq. change from generation to generation, and genotype freq. cannot be calculated by multiplying allele freq., then one of these assumptions is occurring...Evolution • http://study.com/academy/lesson/hardy-weinberg-equilibrium-i-overview.html

45. Selection disrupts HWE

46. Selection • However, selection is not typically that dramatic in a single generation---must build up over many generations

47. Empirical Example • Fruit flies make enzymes that break down alcohol (ADH) • Two ADH alleles in experiment, ADHf and ADHs • Two populations-one fed alcohol food, one normal food • ADHf breaks down ethanol 2x faster than ADHs • Ethanol flies show increase in frequency of ADHf allele, normal food flies remain in HWE

48. Figure 6-14 Selection generally makes it that allele frequencies cannot be calculated under HWE, since it violates the assumption of no selection

49. Testing Predictions with Selection • Flour beetles, have l locus and two alleles, + and l • Genotype ++ and +l are normal, but genotype ll is lethal • This is a recessive lethal • Population started with heterozygotes for l, all +l , so the frequency of each allele is 0.50 • We expect after random mating (100 zygotes) to have • ++ = 25, +l = 50, ll = 25 and all ll die • If each survivor has 10 gametes, then generation 2 will be: 25 ++ = 250 + gametes, no l 50 +l = 250 + gametes, 250 l gametes 750 total gametes, so frequency is + 0.67, l = 0.33

50. Empirical Example Prediction We could calculate this over 12 generations the same Way Prediction is circles, Actual data is triangles This is amazingly accurate!