1. Sources of Variation: Mutation Recombination

2. VII.Mutations I: Changes in Chromosome Number and Structure - Overview:

3. VII.Mutations I: Changes in Chromosome Number and Structure - Overview: 1) A mutation is ….

4. VII.Mutations I: Changes in Chromosome Number and Structure - Overview: 1) A mutation is a change in the genome of a cell.

5. VII.Mutations I: Changes in Chromosome Number and Structure - Overview: 1) A mutation is a change in the genome of a cell. 2) Evolutionarily important mutations are heritable (not somatic). However, the tendency for a gene to mutate in somatic tissue (cancer) as a result of sensitivity to env conditions may be heritable.

6. VII.Mutations I: Changes in Chromosome Number and Structure - Overview: 3) Changes occur at 4 scales (large to small) - Change in the number of SETS of chromosomes (change in PLOIDY) - Change in the number of chromosomes in a set (ANEUPLOIDY: trisomy, monosomy) - Change in the number/arrangement of genes on a chromosome - Change in the nitrogenous base sequence within a gene In general, the LARGER the change, the more dramatic (and usually deleterious) the effects. If you have a functioning genome, a big change is going to be MORE LIKELY to disable it than a small change…

7. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy

8. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms:

9. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: a. Autopolyploidy: production of a diploid gamete used in reproduction within a species. Failure of meiosis I or II 2n gamete Correct meiosis in other parent 1n gamete 3n zygote

10. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: a. Autopolyploidy: production of a diploid gamete used in reproduction within a species. Errors in mitosis can also contribute, in hermaphroditic species

11. 2n 1) Consider a bud cell in the flower bud of a plant.

12. 2n 1) Consider a bud cell in the flower bud of a plant. 4n 2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell.

13. 2n 1) Consider a bud cell in the flower bud of a plant. 4n 2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell. 3) A tetraploid flower develops from this tetraploid cell; eventually producing 2n SPERM and 2n EGG

14. 2n 1) Consider a bud cell in the flower bud of a plant. 4n 2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell. 3) A tetraploid flower develops from this tetraploid cell; eventually producing 2n SPERM and 2n EGG 4) If it is self-compatible, it can mate with itself, producing 4n zygotes that develop into a new 4n species. Why is it a new species?

15. How do we define ‘species’? “A group of organisms that reproduce with one another and are reproductively isolated from other such groups” (E. Mayr – ‘biological species concept’)

16. How do we define ‘species’? Here, the tetraploid population is even reproductively isolated from its own parent species…So speciation can be an instantaneous genetic event… 4n 2n Gametes 2n 4n Zygote 2n 1n Gametes Zygote 2n 3n Triploid is a dead-end… so species are separate

17. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: a. Autopolyploidy: production of a diploid gamete used in reproduction within a species. b. Allopolyploidy: fusion of gametes from different species (hybridization). These are usually sterile because the chromosomes are not homologous and can’t pair during gamete formation. BUT… if the chromosomes replicate and separate without cytokinesis, they create their own homologs and sexual reproduction is then possible.

20. Spartina alterniflora from NA colonized Europe Spartina maritima native to Europe X Spartina anglica – an allopolyploid and a worldwide invasive outcompeting native species Sterile hybrid – Spartina x townsendii Allopolyploidy – 1890’s

21. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: Polyploidy is common in plants; 50% of angiosperm species may be the product of polyploid speciation events.

22. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: Polyploidy is common in plants; 50% of angiosperm species may be the product of polyploid speciation events. In vertebrates, polyploidy decreases in frequency from fish to amphibians to reptiles, and is undocumented in birds. There is one tetraploid mammal. (Red viscacha rat).

23. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism:

24. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: - when the sexes are separate, the rare, random mutation of producing a diploid gamete is UNLIKELY to occur in two parents simultaneously. So, the rare diploid gamete made by one parent (karyokinesis without cytokinesis doubling chromosome number in a cell) will probably fertilize a normal haploid gamete. This produces a TRIPLOID… which may live, but would be incapable of sexual reproduction. 2n 1n 3n

25. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: - unless…. the new organism could ALSO produce eggs without reduction..clonally… and these are the rare animals that we see – triploid ‘species’ that are composed of females that reproduce asexually. (Some may still mate with their diploid ‘sibling’ species so that the sperm stimulated the egg to develop – but without incorporation of sperm DNA.) Like this Blue-spotted Salamander A. laterale, which has a triploid sister species, A. tremblayi

26. C. Inornatus C. neomexicanus C. tigris Parthenogenetic diploid

27. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: - So, in species with separate sexes, polyploidy is probably rare because the typical condition would be TRIPLOIDY, which is usually a sterile condition.

28. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: - So, in species with separate sexes, polyploidy is probably rare because the typical condition would be TRIPLOIDY, which is usually a sterile condition. - But in hermaphroditic organisms (like many plants), a single mutation can affect BOTH male and female gametes.

29. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: SO! Polyploidy may be more frequent in plants because they are hermaphroditic more often than animals; especially vertebrates. Most cases of polyploidy in animals is usually where triploid females survive and reproduce asexually. Also, simpler development in plants means they may tolerate imbalances better.

30. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: 4. Evolutionary Importance: - obviously can be an instant speciation event - polyploidy is also a mechanism for “genome doubling” or “whole genome duplication” - this duplication allows for divergence of copied gene function and evolutionary innovation. Eventually, the copies may be so different that they don’t really represent duplicates any more… resulting in “diploidization”.

33. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy B. Aneuploidy

34. 1. Mechanism: Non-disjunction during gamete formation During either Meiosis I or II, segregation of (homologs or sister chromatids) does not occur; both entities are pulled to the same pole.

35. B. Aneuploidy 1. Mechanism: Non-disjunction during gamete formation During either Meiosis I or II, segregation of (homologs or sister chromatids) does not occur; both entities are pulled to the same pole. This produces gametes with one more (1n + 1) or one less (1n -1) chromosome than they should have. Subsequent fertilization with a normal haploid (1n) gamete produces a trisomy (2n+1) or monosomy (2n-1).

36. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy B. Aneuploidy C. Changes in Gene Number and Arrangement

37. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy B. Aneuploidy C. Changes in Gene Number and Arrangement 1. Deletions and Additions:

38. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy B. Aneuploidy C. Changes in Gene Number and Arrangement 1. Deletions and Additions: a. mechanisms: i. unequal crossing over:

39. i. Unequal Crossing-Over a. process: If homologs line up askew: A ab B

40. A ab B i. Unequal Crossing-Over a. process: If homologs line up askew And a cross-over occurs

41. Aab B i. Unequal Crossing-Over a. process: If homologs line up askew And a cross-over occurs Unequal pieces of DNA will be exchanged… the A locus has been duplicated on the lower chromosome and deleted from the upper chromosome

42. i. Unequal Crossing-Over a. process: b. effects: - can be bad: deletions are usually bad – reveal deleterious recessives additions can be bad – change protein concentration

43. i. Unequal Crossing-Over a. process: b. effects: - can be bad: deletions are usually bad – reveal deleterious recessives additions can be bad – change protein concentration - can be good: more of a single protein could be advantageous (r-RNA genes, melanin genes, etc.)

44. i. Unequal Crossing-Over a. process: b. effects: - can be bad: deletions are usually bad – reveal deleterious recessives additions can be bad – change protein concentration - can be good: more of a single protein could be advantageous (r-RNA genes, melanin genes, etc.) source of evolutionary novelty (Ohno hypothesis - 1970) where do new genes (new genetic information) come from?

45. Gene ADuplicated A Mutation – may even render the protein non-functional But this organism is not selected against, relative to others in the population that lack the duplication, because it still has the original, functional, gene. generations

46. Mutation – may even render the protein non-functional Mutation – other mutations may render the protein functional in a new way So, now we have a genome that can do all the ‘old stuff’ (with the original gene), but it can now do something NEW. Selection may favor these organisms. Gene ADuplicated A generations

47. If so, then we’d expect many different neighboring genes to have similar sequences. And non-functional pseudogenes (duplicates that had been turned off by mutation). These occur – Gene Families

48. And, if we can measure the rate of mutation in these genes, then we can determine how much time must have elapsed since the duplication event… Gene family trees…

49. VII.Mutations I: Changes in Chromosome Number and Structure A. Polyploidy B. Aneuploidy C. Changes in Gene Number and Arrangement 1. Deletions and Additions: a. mechanisms: i. unequal crossing over: (both) ii. Intercalary Deletion A C B

50. 1. Deletions and Additions: a. mechanisms: i. unequal crossing over: (both) ii. Intercalary Deletion A C B

51. 1. Deletions and Additions: a. mechanisms: i. unequal crossing over: (both) ii. Intercalary Deletion A C

52. 1. Deletions and Additions: a. mechanisms: i. unequal crossing over: (both) ii. Intercalary Deletion 1. Deletions and Additions: a. mechanisms: i. unequal crossing over: (both) ii. Intercalary Deletion -recognized by the formation of a ‘deletion loop’ in homolog during synapsis:

53. 1. Deletions and Additions: a. mechanisms: i. unequal crossing over: (both) ii. Intercalary Deletion iii. Transposons (addition) - transposons are copied (replicated) independent of the S phase of interphase…the copy is inserted elsewhere in the genome. Create homologus regions that lead to unequal crossing over and duplications

55. 1. Deletions and Additions: a. mechanisms: i. unequal crossing over: (both) ii. Intercalary Deletion iii. Transposons (addition) - OR, a transposon can be inserted within a gene, destroying it and functionally ‘deleting’ it.

56. VI. Mutation A.Overview B.Changes in Ploidy C.Changes in ‘Aneuploidy’ (changes in chromosome number) D. Change in Gene Number/Arrangement 1.Deletions and Additions 2.Inversion (changes the order of genes on a chromosome)

57. VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement 1.Deletions and Additions 2.Inversion (changes the order of genes on a chromosome)

58. VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement 1.Deletions and Additions 2.Inversion (changes the order of genes on a chromosome) Chromosomes are no longer homologous along entire length B-C-D on top d-c-b on bottom

59. VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement 1.Deletions and Additions 2.Inversion (changes the order of genes on a chromosome) Chromosomes are no longer homologous along entire length ONE “loops” to get genes across from each other… And if a cross- over occurs….

60. The cross-over products are non- functional, with deletions AND duplications VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement 1.Deletions and Additions 2.Inversion (changes the order of genes on a chromosome)

61. The only functional gametes are those that DID NOT cross over – and preserve the parental combination of alleles VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement 1.Deletions and Additions 2.Inversion (changes the order of genes on a chromosome)

62. Net effect: stabilizes sets of genes. This allows selection to work on groups of alleles… those that work well TOGETHER are selected for and can be inherited as a ‘co- adapted gene complex’ VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement 1.Deletions and Additions 2.Inversion (changes the order of genes on a chromosome)

63. VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement 1.Deletions and Additions 2.Inversion (changes the order of genes on a chromosome) 3.Translocation

64. Translocation Downs. Transfer of a 21 chromosome to a 14 chromosome Can produce normal, carrier, and Down’s child.

66. VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement D. Change in Gene Structure 1.Mechanism #1: Exon Shuffling Crossing over WITHIN a gene, in introns, can recombine exons within a gene, producing new alleles. EXON 1aEXON 2aEXON 3a Allele “a” EXON 1AEXON 2AEXON 3A Allele “A”

67. VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement D. Change in Gene Structure 1.Mechanism #1: Exon Shuffling Crossing over WITHIN a gene, in introns, can recombine exons within a gene, producing new alleles. EXON 1aEXON 2aEXON 3a Allele “a” EXON 1AEXON 2AEXON 3A Allele “A” EXON 2aEXON 3a EXON 1A EXON 2AEXON 3A EXON 1a Allele “α” Allele “ά”

68. Throws off every 3-base codon from mutation point onward VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement D. Change in Gene Structure 1. Mechanism #1: Exon Shuffling 2. Mechanism #2: Point Mutations a. addition/deletion: “frameshift” mutations …T C C G T A C G T …. Normal …A G G C A U G C A … ARGHISALA Mutant: A inserted …T C C A G T A C G T …. …A G G U C A U G C A … ARGSERCYS DNA m-RNA

69. VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement D. Change in Gene Structure 1. Mechanism #1: Exon Shuffling 2. Mechanism #2: Point Mutations a. addition/deletion: “frameshift” mutations b. substitution At most, only changes one AA (and may not change it…) … T C C G T A C G T …. Normal …A G G C A U G C A … DNA m-RNA ARGHISALA Mutant: A for G …T C C A T A C G T …. …A G G U A U G C A … ARGTYRALA

70. SOURCES OF VARIATION MUTATION RECOMBINATION ?

71. RECOMBINATION Independent Assortment

72. Independent Assortment produces an amazing amount of genetic variation. Consider an organism, 2n = 4, with two pairs of homologs. They can make 4 different gametes (long Blue, Short Red) (Long Blue, Short Blue), (Long Red, Short Red), (Long Red, Short blue). Gametes carry thousands of genes, so homologous chromosomes will not be identical over their entire length, even though they may be homozygous at particular loci. Well, the number of gametes can be calculated as 2 n or

73. Independent Assortment produces an amazing amount of genetic variation. Consider an organism with 2n = 6 (AaBbCc) …. There are 2 n = 8 different gamete types. ABCabc AbcabC aBCAbc AbCaBc

74. Independent Assortment produces an amazing amount of genetic variation. Consider an organism with 2n = 6 (AaBbCc) …. There are 2 n = 8 different gamete types. And humans, with 2n = 46? ABCabc AbcabC aBCAbc AbCaBc

75. Independent Assortment produces an amazing amount of genetic variation. Consider an organism with 2n = 6 (AaBbCc) …. There are 2 n = 8 different gamete types. And humans, with 2n = 46? 2 23 = ~ 8 million different types of gametes. And each can fertilize ONE of the ~ 8 million types of gametes of the mate… for a total 2 46 = ~70 trillion different chromosomal combinations possible in the offspring. ABCabc AbcabC aBCAbc AbCaBc

76. Independent Assortment produces an amazing amount of genetic variation. And each can fertilize ONE of the ~ 8 million types of gametes of the mate… for a total 2 46 = 70 trillion different chromosomal combinations possible in the offspring. YOU are 1 of the 70 trillion combinations your own parents could have made. IA creates a huge amount of genetic variation, and that doesn’t include crossing over!!!!

77. VII. Mutation A. Changes in Ploidy B Changes in ‘Aneuploidy’ (changes in chromosome number) C. Change in Gene Number/Arrangement D. Change in Gene Structure E. Summary Sources of VariationCauses of Evolutionary Change MUTATION: Natural Selection -New Genes: point mutation Mutation (polyploidy can make new exon shuffling species) RECOMBINATION: - New Genes: crossing over -New Genotypes: crossing over independent assortment

78. SOURCES OF VARIATION MUTATION RECOMBINATION Independent Assortment Crossing Over – New combinations of genes on chromosomes “Hey!! That solves my dilemma about how new variation is produced each generation!! Too bad I’m dead!