Molecular Evolution. H.J. Muller. A.H. Sturtevant. H.J. Muller. A.H. Sturtevant

Transcription

1 Molecular Evolution Arose as a distinct sub-discipline of evolutionary biology in the 1960 s Arose from the conjunction of a debate in theoretical population genetics and two types of data that became readily available in the 1960 s Will exam first the theoretical debate: GENETIC LOAD The Genetic Load Debate Had Its Origins In a Debate That Arose Early in the 20 th Century: A Debate Arising From A Single Drosophila Laboratory: T. H. Morgan s Pithecanthropus A.H. Sturtevant H.J. Muller 1919 This Debate Was Strongly Influenced By The Techniques Available for Scoring Genetic Variation: A Recurrent Theme in Molecular Evolution Pithecanthropus A.H. Sturtevant H.J. Muller

2 Morgan & Muller Scored Variation By Inbreeding Drosophila To Reveal Single Locus Variants With Visible Morphological Effects Inbreeding Wild-Caught Drosophila Revealed Little Variation In Natural Populations For Such Single Locus Visible Variants Classical School Natural Populations Have Very Little Polymorphism. Most Individuals Are Homozygous for a Wildtype Allele. Very Rarely, An Individual Is Heterozygous For A Mutant Allele, Which Is Usually Deleterious. Rarely, A Beneficial Mutation Arises and Then Goes Rapidly To Fixation. Therefore, the Phase of Transient Polymorphism Is Brief. Therefore, The Population Can Be Characterized By A Single Homozygous Wildtype At Most Loci, With Rare Mutants, And Occassional Bursts of Evolution Limited By The Input of New, Beneficial Mutations. 2

3 Sturtevant, As An Undergrad, Came Up With The Idea of A Chromosome Map. He Soon Discovered That Different Strains Had Different Gene Orders: He Had Discovered Paracentric Inversions By Mapping. By the 1930 s, Cytological Techniques Had Been Developed That Allowed The Rapid Scoring of Large Numbers of Individuals for Paracentric Inversions. Sturtevant Recruited A Russian Immigrant, Th. Dobzhansky, To Score Natural Populations With This Technique

4 Dobzhansky & Sturtevant (1936): An Inversion Tree for Drosophila pseudoobscura (A) and D.persimilis (B) Much Intraspecific Polymorphism Each Inversion Mutation Ideally Occurs Only Once in Tree and Tree Minimizes Total Number Of Mutations -- Maximum Parsimony 4

5 Maximum Parsimony (and other techniques) allow you to infer the state of extinct ancestral states. Tree Is Rooted By Looking At a Closely Related Species That Is Known To Be Phylogenetically Outside the Groups of Interest Outgroup Rooting The Inversion Tree Is Not Always The Same As A Tree of Species Or Populations, In This Case Because of: Transpecific Polymorphism 5

6 Balanced School Regarding Each Chromosome Arm As A Locus, Sturtevant and Dobzhansky Concluded That There Is Much Intraspecific Polymorphism. There Are Multiple Alleles, Maintained By Balancing Selection, And No Wildtype. Therefore, Natural Populations Are Highly Polymorphic And Can Rapidly Adapt to Changing And Spatially Heterogeneous Environments By Using This Vast Pool of Polymorphic Variation. Genetic Load In 1950, Muller Wrote A Highly Influential Paper Entitled Our Load of Mutations Muller s Model Mutation: From Wildtype A to Deleterious Mutant a: A a at rate µ Fitness Model: AA Aa aa» s Assuming Random Mating, Input Rate of a is µ, and Output Rate Is sq 2 At Equilibrium, Input = Output µ = sq 2 q eq = µ/s W=p 2 (1)+2pq(1)+q 2 (1-s)=1-q 2 s=1- µ at Equil. 6

7 Muller s Model Load Is Independent of s and Is A Function Only Of µ Haldane: Substitutional Load Mutation: From Wildtype a to Beneficial Mutant A: a A Fitness Model: AA Aa aa» 1+s 1+s/2 1 Assuming Random Mating, At Equilibrium, p=1 W max =1+s Load=W max -W L=1+s-[1+p 2 s+pqs] L=s(1-p) L=Excess Reproduction Needed To Go From p to p eq =1 Haldane: Substitutional Load Load Is Independent of s! 7

8 Haldane: Substitutional Load p 0 =1/(2N) for a new mutant. Letting p 0 =10-6 (N=500,000) The Load = 30. Haldane argued that a population could tolerate no more than a 10% demand of excess reproduction. Using L=30, this means a population can tolerate no more than one locus undergoing a beneficial substitution every 300 generations. This means that very few transient polymorphisms can exist in a population at any given time. Crow & Kimura: Balanced Load Fitness Model: AA Aa aa» 1-s 1 1-t Assuming Random Mating, At Equilibrium, p eq =t/(s+t) W max =1 (fitness of Aa) Load=(W max -W)/W max =sp 2 +tq 2 At Equilibrium, L=st/(s+t) Letting s=t=0.1, L=0.05 (5% fitness reduction) For n balanced, independently acting loci: This means that very few balanced polymorphisms can exist in a population at any given time. Genetic Load The Conclusions From Load Theory Strongly Supported The Classical School and Were Against The Balanced School 8

9 Two Types Of Data Became Widely Available in the 1960 s Amino Acid Sequence Data (Primarily documenting substitutions between species) Protein Electrophoresis Data (Primarily documenting polymorphisms within species) Amino Acid Sequence Data There were two many substitutions to be consistent with load theory Motto Kimura solved this problem with load theory (Nat. 217: , 1968) Neutral Theory The Classical School Allowed Two Types of Mutations: Rarely Occurring Deleterious Mutations Extremely Rare Beneficial Mutations That Go To Rapid Fixation and Become the Wildtype Allele Kimura s Neutral Theory Added A Third Mutational Class To The Classical School Model: Neutral Mutations Of The Wildtype Allele That Have No Impact on Fitness As A Result, The Wildtype Allele Is Now Replaced By A Set of Functionally Equivalent Alleles; That is, there is no longer a wildtype allele, but a wildtype set of neutral alleles Note: The Neutral Model Does NOT Assume That All Mutations Are Neutral, But Rather Accepts The Classical School Model for Non-Neutral Mutations. 9

10 Neutral Theory Genetic Drift Determines the Rate of Loss = 1 / 2N Mutation Determines the Rate of Input = (2N)µ Rate of Evolution =Rate of Input X Rate of Loss = (2N)µ 1 / 2N = µ Note: The Rate of Neutral Evolution Does Not Depend upon Population Size. All populations, regardless of size, have an innate tendency to evolve as driven by mutation and drift. Moreover, if the neutral mutations rates are comparable, this tendency is just as strong in a large population as in a small population. GENETIC DRIFT IS IMPORTANT FOR ALL POPULATIONS! ALSO, THE NEUTRAL MODEL EXPLAINS THE HIGH RATE OF AMINO ACID SUBSTITUTION IN A LOAD- FREE FASHION! Because The Neutral Theory Accepts That Many Mutations Are Deleterious, This Theory Could Also Explain the Heterogeneity In Substitution Rates Observed in Different Proteins Neutral Theory Amino Acid Sequence Data α-hb Data The Substitutions Seemed To Define A Molecular Clock (King & Jukes, Sci. 154: ,1969). This Also Seemed To Support Kimura s Theory Because It Predicted The Rate of Substitution= µ, which was usually treated as a constant. 10

11 Protein Electrophoresis Data Protein Electrophoresis Data Lewontin & Hubby (Genetics 54: , 1966), Johnson et al. (Studies in Genetics. III: , 1966), and Harris (Proceedings of the Royal Society of London B 164: ) showed that about 1/3 of all protein coding loci were polymorphic for electrophoretically detectable alleles in Drosophila and in humans This frequency was much too high for Load Theory Kimura and Ohta (Nat. 229: , 1971) once again rescued the Classical School with the Neutral Theory Kimura & Ohta Time Period of Transient Polymorphism 1/(2N) of Neutral Mutations Go To Fixation and Transiently Contribute To Polymorphism Levels Most Neutral Mutations Are Lost and Contribute Little to Polymorphism Levels 11

12 Kimura & Ohta The Neutral Theory Dominated The Field of Molecular Evolution Throughout the 70 s and Motivated Studies Both Pro and Con Difficulties For The Neutral Theory J. Maynard Smith (Am. Nat. 104: , 1970): Substitution Rate Studies Required µ between 10-5 to If N=10-6, Then H eq =40/(40+1)=0.98. Therefore, there was too little heterozygosity under the neutral theory. There was also too little a range in heterozygosity under the neutral theory. 12

13 Difficulties For The Neutral Theory Most Observations Below This Threshold This Implies A Small Range of Population Sizes, and That Almost All Species Have N < 5,000 (Including Insects & Bacteria). Ohta ( ) Created The Nearly Neutral Theory To Explain The Heterozygosity Observations Showed That Genetic Drift Determines Evolutionary Dynamics For Any Mutation With s <1/(2N ev ) Let µ(s) describe the probability of a mutation having selection coefficient s, then The neutral mutation rate=µ neutral = As N ev, µ neutral This explains why Heterozygosity levels off and has a narrow range (recall θ=4nµ neutral ) Unfortunately, this also means you lose the molecular clock because the rate of substitution is now a function of N ev Kimura At First Strongly Opposed Ohta s Departure From Pure Neutrality, But Embraced It in 1979 Kimura (PNAS 76: , 1979): Assume µ is constant per generation (previously, he had assumed it was constant in absolute time in order to explain the clock) Let t = generation time, so µ/t is the mutation rate in absolute time Assuming a specific model for µ(s) (on the basis of no data), and assuming that Can get µ neutral /t = Constant and Therefore Have Clock This paper was poorly received because of the highly contrived nature of its assumptions. Kimura even removed this paper from his lifetime list of papers. 13

14 Molecular Evolution Is Thriving, But Genetic Load Has Been Discredited Much of the theory was an artifact of using relative fitnesses and ridiculous W max s (e.g., the future population with p=1 in substitutional load; the individual heterozygous for all loci in the balanced load) More realistic fitness models have no load at all Molecular Evolution Is No Longer Dominated By the Neutral Theory Much of the good fit of the clock was an artifact; More rigorous tests show frequent violations of Kimura s Poisson Clock Still Cannot Simultaneously Explain Substitution Rates and Heterozygosity Now Have Better Tests of Selection: E.g., Fay et al (Nature 415: ) Found evidence for positive and balancing selection in 60% of the protein coding genes in D. melanogaster, far higher than permitted by the neutral theory of molecular evolution. The neutral theory is still a widely used null hypothesis in molecular evolution Molecular Evolution Now Focuses On Problem Areas Without A Single Dogma Dominating the Field 1) Gene and Genome Evolution What kinds of evolutionary changes occur in various genes and genome types and what evolutionary forces are involved? 2) Organismal Evolution Use the results of studies on genes and genomes to study and test hypotheses about organismal micro- and macro-evolution 3) Population Genetics Describe the amount and distribution of molecular variation within a species and test and detect the evolutionary forces responsible 4) Quantitative Genetics Use molecular genetics to understand the genetic basis of phenotypic variation 5) Phylogenetics Reconstruct the evolutionary history of species, and help determine species status 14

15 The Field of Molecular Evolution Has Undergone A Metamorphosis, And It Is Much Stronger For It And More Relevant Than Ever To Many Basic Problems in Biology 15