1. Evolutionary Genetics

2. I.Speciation A. Definition: Mayr’s ‘biological species concept’ – “a group of actually or potentially interbreeding organisms that is reproductively isolated from other such groups”.

3. Evolutionary Genetics I.Speciation A. Definition: Mayr’s ‘biological species concept’ – “a group of actually or potentially interbreeding organisms that is reproductively isolated from other such groups”. - only appropriate for sexually reproducing species - Reproductive isolation will inevitably lead to greater genetic divergence (even just by chance), and an increased likelihood of genetic uniqueness/incompatibility.

4. Evolutionary Genetics I.Speciation II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat)

5. Drosophila speciation on the Hawaiian Islands. Obbard D J et al. Mol Biol Evol 2012;29:3459-3473 © The Author 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Recent divergences involve a specie colonizing a new island (Hawai’i); older divergence occurred in the past, when older islands first crested above the ocean and were made available for colonization.

7. Vicariance – the splitting of a range by a new geographic feature, such as a river or land mass (next).

8. Almost all most recent divergence events date to 3 my, and separate species on either side of the isthmus; suggesting that the formation of the isthmus was a cause of speciation in all these species pairs. Snapping ‘Pistol’ Shrimp

9. Mayr – Peripatric Speciation Small population in new environment; the effect of drift and selection will cause rapid change, resulting in a speciation event.

10. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation

11. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates Western MeadowlarkEastern Meadowlark

12. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates 4. Mechanical isolation - genitalia don't fit; limit pollinators You’re crazy… You’re cute…

13. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates 4. Mechanical isolation - genitalia don't fit; limit pollinators 5. Gametic Isolation - gametes transferred but sperm can't fertilize egg; this is a common isolation mechanism in species that spawn at the same time

14. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers B. Post-Zygotic Isolation

15. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies

16. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies 2. Hybrid Inviability - F1 has lower survival Crazy hybrids A ‘zedonk’

17. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies 2. Hybrid Inviability - F1 has lower survival 3. Hybrid Sterility - F1 has reduced reproductive success Horse: 64 chromosomes Donkey: 62 chromosomes Mule: 63 non-homologous chromosomes

18. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies 2. Hybrid Inviability - F1 has lower survival 3. Hybrid Sterility - F1 has reduced reproductive success 4. F2 breakdown - F1's survive but F2's have incompatible combo's of genes

19. AABB x aabb F1: AaBb = ok F2: A-B- = ok A-bb = no aaB- = no aabb = ok

20. Evolutionary Genetics II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates 4. Mechanical isolation - genitalia don't fit; limit pollinators 5. Gametic Isolation - gametes transferred but sperm can't fertilize egg; this is a common isolation mechanism in species that spawn at the same time B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies 2. Hybrid Inviability - F1 has lower survival 3. Hybrid Sterility - F1 has reduced reproductive success 4. F2 breakdown - F1's survive but F2's have incompatible combo's of genes All of these – except geographic isolation - are fundamentally genetic in nature because physiology (gametic), morphology (mechanical), and behavior (temporal and behavioral) have a genetic component. Obviously, the post-zygotic barriers are entirely genetic. Speciation is the process of creating a genetically distinct population, which maintains its distinction in the face of possible hybridization.

21. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation - Evolution and speciation are not the same: Evolution is a change in the genetic structure of a population Speciation is the establishment of reproductive isolation between populations.

22. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation - Evolution and speciation are not the same: Evolution is a change in the genetic structure of a population Speciation is the establishment of reproductive isolation between populations. - Two populations can evolve over time, but maintain gene flow and not speciate. - Two populations can become geographically isolated and be ‘good species’, while being genetically similar.

23. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation - Evolution and speciation are not the same: Evolution is a change in the genetic structure of a population Speciation is the establishment of reproductive isolation between populations. - Two populations can evolve over time, but maintain gene flow and not speciate. - Two populations can become geographically isolated and be ‘good species’, while being genetically similar. - Small genetic differences can create genomic incompatibility, change in genitalia, or behavioral differences that cause speciation. So, while increasing genetic divergence increases the probability of speciation, small changes can cause reproductive isolation, too.

24. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - rate of mutation, introducing new variation (AIDS virus – error-prone reverse transcriptases introduce many mutations each generation, changing the surface proteins and making it very hard for our immune systems to eliminate all of them.)

25. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - rate of mutation, introducing new variation - size of the population (freq of new allele = 1/2N; so a mutation in a small population will be at a higher frequency that it would be in a large population)

26. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - rate of mutation, introducing new variation - size of the population - effect of this variation (deleterious and adaptive mutations will change frequency rapidly in response to selection; neutral variation will change by drift, alone.)

27. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - rate of mutation, introducing new variation - size of the population - effect of this variation - rate of reproduction of the population Populations with high reproductive rates should change faster that populations with low reproduction rates.

28. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - patterns: As a result of the sequencing boom that began in the 1960’s, biologists realized that there was an extraordinary amount of genetic variation in most populations – variation at the molecular level in DNA sequence. - On average, About 20-30% of all loci are polymorphic (have at least 2 alleles with frequencies over 1%). - D. melanogaster has 10,000 loci, so 3000 are polymorphic. - At these polymorphic loci, Heterozygosity = 0.33

29. Variation in the alcohol dehydrogenase gene, fixed in different populations of Drosophila melanogaster This is the only variation that changes an amino acid; all others are ‘silent’

30. The frequency of different disease-causing mutations in the CFTR gene. Each different mutation is a different allele; most of them are very rare (<1.0%), and all of them are deleterious so selection keeps them rare.

31. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - patterns: As a result of the sequencing boom that began in the 1960’s, biologists realized that there was an extraordinary amount of genetic variation in most populations – variation at the molecular level in DNA sequence. - On average, About 20-30% of all loci are polymorphic (have at least 2 alleles with frequencies over 1%). - D. melanogaster has 10,000 loci, so 3000 are polymorphic. - At these polymorphic loci, Heterozygosity = 0.33 Selection can’t maintain all this heterozygosity (like with sickle cell); we would each be homozygous for at least one deleterious recessive and have reduced fitness. Something ELSE must be maintaining this variation….. Motoo Kimura suggested that most variation was neutral, maintained by drift.

32. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - patterns: - Predictions of the Neutral Model: Rates of substitution should be higher in non-functional (neutral) regions of proteins, in introns, and in the third position of codons, because changes here are neutral. - CONFIRMED

33. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - patterns: - Predictions of the Neutral Model: Rates of substitution should be higher in non-functional (neutral) regions of proteins, in introns, and in the third position of codons, because changes here are neutral. – CONFIRMED The rate of molecular evolution (substitutions) should be independent of the rate of morphological change; a species that changes slowly morphologically can still be changing as rapidly, genetically, as a species that changes fast morphologically. - CONFIRMED

34. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - patterns: - Predictions of the Neutral Model: Rates of substitution should be higher in non-functional (neutral) regions of proteins, in introns, and in the third position of codons, because changes here are neutral. – CONFIRMED The rate of molecular evolution (substitutions) should be independent of the rate of morphological change; a species that changes slowly morphologically can still be changing as rapidly, genetically, as a species that changes fast morphologically. – CONFIRMED The rate of substitution of one allele in a population by another allele should occur at a constant rate – a molecular ‘clock’ - CONFIRMED.

35. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - patterns: - Predictions of the Neutral Model: - Problem: In the neutral model, mutations should accumulate at a constant rate…but constant in relative time – relative to the generation time of the organism. Species with short generation times should accumulate changes more rapidly than species that have longer generation times. This is true for non-coding DNA, as expected for neutral DNA. But it is NOT true for proteins and protein coding sequences, where AA substitution rates are constant in absolutely time across species – suggesting that some selection is acting. Ohta’s “nearly neutral” model

36. The Nearly Neutral Model (Ohta) - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. Sub. Rate Short GEN TIMELong EXP. OBS.

37. The Nearly Neutral Model (Ohta) SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. - So, something must be 'slowing down' this rate of substitution in species with short gen. times. What's slowing it down is their large populations size, such that the effects of drift, alone, are reduced. Sub. Rate Short GEN TIMELong EXP. OBS. LARGE POP. SIZE

38. The Nearly Neutral Model (Ohta) SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. - So, something must be 'slowing down' this rate of substitution in species with short gen. times. What's slowing it down is their large populations size, such that the effects of drift, alone, are reduced. - Likewise, species with long generation times have small populations, and substitution by drift and fixation is more rapid than expected based on generation time, alone. Sub. Rate Short GEN TIMELong EXP. OBS. SMALL POP. SIZE

39. The Nearly Neutral Model (Ohta) SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. - So, something must be 'slowing down' this rate of substitution in species with short gen. times. What's slowing it down is their large populations size, such that the effects of drift, alone, are reduced. - Likewise, species with long generation times have small populations, and substitution by drift and fixation is more rapid than expected based on generation time, alone. Sub. Rate Short GEN TIMELong EXP. OBS. SMALL POP. SIZE SO. - The constant rate of AA substitution across species is due to the balance between generation time and population size.

40. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution C. Using Molecular Clocks - the more differences there are, the more time must have elapsed since a common ancestor for these differences to accumulate. - If we know the rate of change for a given set of genes or proteins, then we can estimate the absolute time since divergence.

42. >Arabidopsis MASFDEAPPGNPKAGEKIFRTKCAQCHTVEKGAGHKQGPNLNGLFGRQSGTTPGYSYSAA NKSMAVNWEEKTLYDYLLNPKKYIPGTKMVFPGLKKPQDRADLIAYLKEGTA >Euglena GDAERGKKLFESRAGQCHSSQKGVNSTGPALYGVYGRTSGTVPGYAYSNANKNAAIVWED ESLNKFLENPKKYVPGTKMAFAGIKAKKDRLDIIAYMKTLKD >Hippo GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQSPGFSYTDANKNKGITWG EETLMEYLENPKKYIPGTKMIFAGIKKKGERADLIAYLKQATNE >Mosquito MGVPAGDVEKGKKLFVQRCAQCHTVEAGGKHKVGPNLHGLFGRKTGQAAGFSYTDANKAK GITWNEDTLFEYLENPKKYIPGTKMVFAGLKKPQERGDLIAYLKSATK >Rice MASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTA NKNMAVIWEENTLYDYLLNPKKYIPGTKMVFPGLKKPQERADLISYLKEATS Sequences of cytochrome c from NCBI

43. Euglena Mosquito Hippo Rice Arabidopsis

45. Unresolved molecular phylogenies of gibbons and siamangs (Family: Hylobatidae) based on mitochondrial, Y-linked, and X-linked loci indicate a rapid Miocene radiation or sudden vicariance event Molecular Phylogenetics and Evolution, Volume 58, Issue 3, March 2011, Pages 447-455 H. Israfil, S.M. Zehr, A.R. Mootnick, M. Ruvolo, M.E. Steiper

46. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution C. Using Molecular Clocks D. Concordant Phylogenies

47. IF species are descended from common ancestors (like people in a family), and IF we know the rate of genetic change (mutation), THEN we should be able to compare genetic similarity and predict when common ancestors lived. AND, if the fossil record is also a product of evolution, THEN the species though to be ancestral to modern groups should exist at this predicted age, too. In other words, we should be able to compare DNA and protein sequences in living species and predict where, in the sedimentary strata of the Earth’s crust, a third different species should be. D. Concordant Phylogenies

48. Clustering analysis based on amino acid similarity across seven proteins from 17 mammalian species. D. Concordant Phylogenies

49. Now, we date the oldest mammalian fossil, which our evolution hypothesis dictates should be ancestral to all mammals, both the placentals (species 1-16) and the marsupial kangaroo. …. This dates to 120 million years 16 D. Concordant Phylogenies

50. And, through our protein analysis, we already know how many genetic differences (nitrogenous base substitutions) would be required to account for the differences we see in these proteins - 98. 16 D. Concordant Phylogenies

51. So now we can plot genetic change against time, hypothesizing that this link between placentals and marsupials is ancestral to the other placental mammals our analysis. 16 D. Concordant Phylogenies

52. Now we can test a prediction. IF genetic similarity arises from descent from common ancestors, THEN we can use genetic similarity to predict when common ancestors should have lived... 16 D. Concordant Phylogenies

53. This line represents that prediction. Organisms with more similar protein sequences (requiring fewer changes in DNA to explain these protein differences) should have more recent ancestors... 16 D. Concordant Phylogenies

54. And the prediction here becomes even MORE precise. For example, we can predict that two species, requiring 50 substitutions to explain the differences in their proteins, are predicted to have a common ancestor that lived 58-60 million years ago... 16 D. Concordant Phylogenies

55. Let’s test that prediction. Rabbits and the rodent differ in protein sequence to a degree requiring a minimum of 50 nucleotide substitutions... Where is the common ancestor in the fossil record? D. Concordant Phylogenies

56. Just where genetic analysis of two different EXISTING species predicts. 16 D. Concordant Phylogenies

57. OK, but what about all of our 16 "nodes"? Evolution predicts that they should also exist on or near this line.... 16 D. Concordant Phylogenies

58. And they are. Certainly to a degree that supports our hypothesis based on evolution. Concordance between molecular clocks and the geologic record

59. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution C. Using Molecular Clocks D. Concordant Phylogenies E. Rates of Speciation - Speciation can be an instantaneous genetic event – through polyploidy, or mutation that affects specific genes important in forming a reproductive isolating barrier.

60. Evolutionary Genetics II. Making Species - Reproductive Isolation III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution C. Using Molecular Clocks D. Concordant Phylogenies E. Rates of Speciation - Speciation can be an instantaneous genetic event – through polyploidy, or mutation that affects specific genes important in forming a reproductive isolating barrier. - But speciation can also be a continuous process, reflecting the accumulation of genetic differences. Still, these differences might accumulate at a steady rate or at episodic rates.

62. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 1. Consider a large, well-adapted population

63. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 1. Consider a large, well-adapted population Effects of Selection and Drift are small - little change over time

64. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 2. There are always small sub-populations "budding off" along the periphery of a species range...

65. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 2. Most will go extinct, but some may survive... X X X

66. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 2. These surviving populations will initially be small, and in a new environment...so the effects of Selection and Drift should be strong... X X X

67. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 3. These populations will change rapidly in response... X X X

68. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 3. These populations will change rapidly in response... and as they adapt (in response to selection), their populations should increase in size (because of increasing reproductive success, by definition). X X X

69. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 3. As population increases in size, effects of drift decline... and as a population becomes better adapted, the effects of selection decline... so the rate of evolutionary change declines... X X X

70. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 4. And we have large, well-adapted populations that will remain static as long as the environment is stable... X X X

71. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 5. Since small, short-lived populations are less likely to leave a fossil, the fossil record can appear 'discontinuous' or 'imperfect' X X X

72. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 5. Large pop's may leave a fossil.... X X X

73. - 1972 - Eldridge and Gould - Punctuated Equilibrium 5. Small, short-lived populations probably won't... X TIME VARIATION X X

74. - 1972 - Eldridge and Gould - Punctuated Equilibrium 6. So, the discontinuity in the fossil record is an expected result of our modern understanding of how evolution and speciation occur... X X X TIME VARIATION

75. - 1972 - Eldridge and Gould - Punctuated Equilibrium TIME VARIATION 6. both in time (as we see), and in SPACE (as changing populations are probably NOT in same place as ancestral species). X X X

76. Darwin’s Dilemmas: Evolution of Complex Traits: 1. Structures with mutually dependent parts CAN evolve through a stepwise process

77. Darwin’s Dilemmas: Evolution of Complex Traits: 2. Structures may have evolved for other selective reasons than we observe now. Ornamentation and attraction homeothermy flight

78. Darwin’s Dilemmas: Evolution of Complex Traits: Source of Heritable Variation: …. Genetics! Nice Job ! You, too!

79. Darwin’s Dilemmas: Evolution of Complex Traits: Source of Heritable Variation: Discontinuity of Fossil Lineages: TIME VARIATION Peripatric Speciation and Punctuated Equilibrium Genetics has tested and confirmed Darwin’s ideas and solved his dilemmas