1. BIOE 109 Summer 2009 Lecture 4- Part I Mutation and genetic variation

2. 1.Mutation 2. Gene Flow 3. Genetic drift 4. Natural selection Four basic processes that can explain evolutionary changes:

3. Sources of genetic variation 1.Crossing over during meiosis- creates new combinations of alleles on individual chromosomes 2. Independent assortment- creates new combinations chromosomes in the daughter cells

4. Sources of genetic variation 1.Crossing over during meiosis- creates new combinations of alleles on individual chromosomes 2. Independent assortment- creates new combinations chromosomes in the daughter cells 3. Mutations- create completely new alleles and genes

5. General classes of mutations

6. General classes of mutations Point mutations “Copy-number” mutations Chromosomal mutations Genome mutations

7. Point mutations

8. Point mutations There are four categories of point mutations:

9. Point mutations There are four categories of point mutations: 1. transitions (e.g., A  G, C  T)

10. Point mutations There are four categories of point mutations: 1. transitions (e.g., A  G, C  T) 2. transversions (e.g., T  A, C  G)

11. Point mutations There are four categories of point mutations: 1. transitions (e.g., A  G, C  T) 2. transversions (e.g., T  A, C  G)

12. Point mutations There are four categories of point mutations: 1. transitions (e.g., A  G, C  T) 2. transversions (e.g., T  A, C  G) 3. insertions (e.g., TTTGAC  TTTCCGAC)

13. Point mutations There are four categories of point mutations: 1. transitions (e.g., A  G, C  T) 2. transversions (e.g., T  A, C  G) 3. insertions (e.g., TTTGAC  TTTCCGAC) 4. deletions (e.g., TTTGAC  TTTC)

14. Point mutations There are four categories of point mutations: 1. transitions (e.g., A  G, C  T) 2. transversions (e.g., T  A, C  G) 3. insertions (e.g., TTTGAC  TTTCCGAC) 4. deletions (e.g., TTTGAC  TTTC) in coding regions, point mutations can involve silent (synonymous) or replacement (nonsynonymous) changes.

15. Point mutations There are four categories of point mutations: 1. transitions (e.g., A  G, C  T) 2. transversions (e.g., T  A, C  G) 3. insertions (e.g., TTTGAC  TTTCCGAC) 4. deletions (e.g., TTTGAC  TTTC) in coding regions, point mutations can involve silent (synonymous) or replacement (nonsynonymous) changes. in coding regions, insertions/deletions can also cause frameshift mutations.

16. Loss of function mutations in the cystic fibrosis gene

17. “Copy-number” mutations

18. “Copy-number” mutations these mutations change the numbers of genetic elements.

19. “Copy-number” mutations these mutations change the numbers of genetic elements. gene duplication events create new copies of genes.

20. “Copy-number” mutations these mutations change the numbers of genetic elements. gene duplication events create new copies of genes. one important mechanism generating duplications is unequal crossing over.

21. Unequal crossing-over can generate gene duplications

23. lethal?   neutral?

24. “Copy-number” mutations these mutations change the numbers of genetic elements. gene duplication events create new copies of genes. one mechanism believed responsible is unequal crossing over. over time, this process may lead to the development of multi-gene families.

25. Chromosome 11 Chromosome 16  and  -globin gene families

26. Timing of expression of globin genes

27. Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns!

28. Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba

29. Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba Alcohol dehydrogenase (Adh)  Chromosome 2Chromosome 3

30. Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba Alcohol dehydrogenase (Adh)  Chromosome 2Chromosome 3  mRNA

31. Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba Alcohol dehydrogenase (Adh)  Chromosome 2Chromosome 3  mRNA  cDNA

32. Retrogenes may also be created retrogenes have identical exon structures to their “progenitors” but lack introns! Example: jingwei in Drosophila yakuba Alcohol dehydrogenase (Adh)  Chromosome 2Chromosome 3  mRNA  cDNA  “jingwei”

33. Whole-genome data yields data on gene families

34. “Copy-number” mutations transposable elements (TEs) are common.

35. “Copy-number” mutations transposable elements (TEs) are common. three major classes of TEs are recognized:

36. “Copy-number” mutations transposable elements (TEs) are common. three major classes of TEs are recognized: 1. insertion sequences (700 – 2600 bp)

37. “Copy-number” mutations transposable elements (TEs) are common. three major classes of TEs are recognized: 1. insertion sequences (700 – 2600 bp) 2. transposons (2500 – 7000 bp)

38. “Copy-number” mutations transposable elements (TEs) are common. three major classes of TEs are recognized: 1. insertion sequences (700 – 2600 bp) 2. transposons (2500 – 7000 bp) 3. retroelements

39. Chromosomal inversions lock blocks of genes together

40. Inversions act to suppress crossing-over…  inviable

41. Inversions act to suppress crossing-over… … and can lead to co-adapted gene complexes  inviable

42. Chromosomal inversions in Drosophila pseudoobscura Here is a standard/arrowhead heterozygote:

43. Here are more inversion heterzygotes:

44. Chromosomal translocations are also common

45. Changes in chromosome number are common

46. in mammals, chromosome numbers range from N = 3 to N = 42.

47. Changes in chromosome number are common in mammals, chromosome numbers range from N = 3 to N = 42. in insects, the range is from N = 1(some ants) to N = 220 (a butterfly)

48. Changes in chromosome number are common in mammals, chromosome numbers range from N = 3 to N = 42. in insects, the range is from N = 1(some ants) to N = 220 (a butterfly) karyotypes can evolve rapidly!

49. Muntiacus reevesi Muntiacus muntjac

50. Muntiacus reevesi; N = 23 Muntiacus muntjac; N = 4

51. Genome mutations

52. polyploidization events cause the entire genome to be duplicated.

53. Genome mutations polyploidization events cause the entire genome to be duplicated. polyploidy has played a major role in the evolution of plants.

54. Genome mutations polyploidization events cause the entire genome to be duplicated. polyploidy has played a major role in the evolution of plants. ancient polyploidization events have also occurred in most animal lineages.

55. Generation of a tetraploid

56. Where do new genes come from?

57. An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni

58. Where do new genes come from? An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni Reference: Chen et al. 1997. Proc. Natl. Acad. Sci. USA 94: 3811

59. Where do new genes come from? An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni antifreeze proteins allow these fishes to inhabit subzero sea temperatures.

60. Where do new genes come from? An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni antifreeze proteins allow these fishes to inhabit subzero sea temperatures. act by inhibiting the growth of ice crystals.

61. Where do new genes come from? An example: the antifreeze glycoprotein (AFGP) gene in the Antarctic fish, Dissostichus mawsoni antifreeze proteins allow these fishes to inhabit subzero sea temperatures. act by inhibiting the growth of ice crystals. the AFGP gene dates to ~10 – 14 million years ago (when Antarctic ocean began to freeze over).

62. Where do new genes come from? Step 1. Duplication of the pancreatic trypsinogen gene (6 exons long).

63. Where do new genes come from? Step 1. Duplication of the pancreatic trypsinogen gene (6 exons long). Step 2. Deletion of exons 2 – 5.

64. see Chen et al. 1997. Proc. Natl. Acad. Sci. USA 94: 3811

66. Where do new genes come from? Step 1. Duplication of the pancreatic trypsinogen gene (6 exons long). Step 2. Deletion of exons 2 – 5. Step 3. Expansion of Thr-Ala-Ala triplet 41 times at junction of exon 1.

67. see Chen et al. 1997. Proc. Natl. Acad. Sci. USA 94: 3811

68. Where do new genes come from? Step 1. Duplication of the pancreatic trypsinogen gene (6 exons long). Step 2. Deletion of exons 2 – 5. Step 3. Expansion of Thr-Ala-Ala triplet 41 times at junction of exon 1. Step 4. Expression of AFGP gene in liver, release into blood.

69. Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida

70. the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif!

71. Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif! appears to have evolved independently because:

72. Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif! appears to have evolved independently because: 1. flanking regions show no homology to trypsinogen

73. Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif! appears to have evolved independently because: 1. flanking regions show no homology to trypsinogen 2. different number and locations of introns

74. Convergent evolution of an AFGP gene in the arctic cod, Boreogadus saida the AFGP gene in B. saida also has a Thr-Ala-Ala repeating motif! appears to have evolved independently because: 1. flanking regions show no homology to trypsinogen 2. different number and locations of introns 3. codons used in repeating unit are different