History of. Charles Darwin ( ) Today s OUTLINE: Evolutionary Thought: The Grand Evolutionary Synthesis. Carol Eunmi Lee 9/13/17

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1 Today s OUTLINE: History of Evolutionary Thought: The Grand Evolutionary Synthesis (1) The Sources of Confusion (2) Reconciling Mendel and Darwin (3) The Main Tenets of the Evolutionary Synthesis (4) Key Developments since the Synthesis Dr. Carol Eunmi Lee University of Wisconsin, Madison (5) Gaps in our Understanding Today Charles Darwin ( ) Darwin s contribution: Population Speciation as a result of Natural Selection Last time we discussed Darwin s contributions to evolutionary thinking More offspring are produced than can survive Limited resources and competition for resources There is heritable variation in a population Individuals better adapted to environment survive Survivors leave more offspring ( Survival of the Fittest ) Thus, average character of population is altered But, Darwin s theory was not complete Because Darwin knew nothing about mutation, he had no idea how variation was generated in populations Because Darwin knew nothing about genetics or genes, he had no idea how variation was passed on to offspring (Mendel) Darwin did not know about nonadaptive evolutionary forces, such as Genetic Drift Mendel s work held part of the key to what was missing in Darwin s Theory Mendel published in 1865 was ignored until 1900 Presented a mechanism for how traits got passed on Individuals pass alleles on to their offspring intact (the idea of particulate (genes) inheritance) Title goes here 1

2 Rediscovery of Mendel s laws of inheritance In 1900, Mendel s laws of inheritance were rediscovered Dutch biologist Hugo de Vries, German plant geneticist Carl Correns, and Austrian plant breeder Erich von Tschermak-Seysenegg Worked out laws of inheritance independently Discovered Mendel s work as they were publishing their own Formed the beginning of the foundation of Genetics: Mendel is considered the Father of Genetics Hardy-Weinburg Equilibrium (Lecture 3) Wilhem Weinberg January 13, 1908 G. H. Hardy July 10, 1908 in Science Could mathematically show expectations of Mendelian inheritance and whether expectations are realized in nature BUT Mendel and Darwin s ideas seemed Incompatible PROBLEMS! Mendel s principles: dealt with particulate (discrete) traits (e.g. yellow vs. green, wrinkled vs. smooth) BUT, Darwin observed continuous traits (e.g. beak size, body length) Q: So, how would continuous traits get passed on? Selection vs Mutations Mutations discovered after 1900 Q: If mutations are arising, why need selection... if things are just mutating? Controversy between Mutationists vs Darwinists Mutationists (+ Mendelianism) They thought that evolution required only mutations and passing on of discrete traits Darwinists They thought that evolution required only Natural Selection on continuous variation Title goes here 2

3 Discrete vs Quantitative Traits Darwin was unable to clearly see the pattern of inheritance because he studied quantitative variation Discrete trait: a trait that has distinct values, rather than a range of phenotypes, usually encoded by one or a few genes. Examples: number of fingers, color of Mendel s peas, sickle cell anemia, ABO blood type, number of eggs in a bird clutch, presence/absence of human widow s peak, presence/absence of dimples, etc. Quantitative (continuous) trait: a trait that has a continuum of phenotypes and is encoded by multiple genes. Examples: body size, height, weight, intelligence (IQ), Running speed, beak shape, hair color, skin color, milk yield of cows, lifespan, etc. Frequency Frequency Type Type Proponents of the Darwinist Theory Proponents of Darwinism were correct about mechanisms of Natural Selection, but they did not understand what Selection was acting on, as they were unaware of the unit of inheritance (genes) or how the variation was passed on to the next generation They came up with the idea of Blending inheritance where offspring gain characteristics of both parents, like mixing colors of paint but, this was a vague idea that was incorrect Many of them were Biometricians (statistical types) that thought that evolution was gradually acting on continuous traits Proponents of the Mutationist/Mendelist Theory Many Prominent Geneticists at the time supported the Mutationist/Mendelist theory Proponents of the mutationist theory included Hugo de Vries, among those who discovered Mendel s 1900 paper and Thomas Hunt Morgan, founder of Drosophila genetics Thought that evolution arose through genetic changes (mutations) that were discrete and sudden Controversy between Mutationists vs Darwinists Controversy persisted for ~30 years up till the 1930s, during which little progress was made New species originated when they mutated from pre-existing species, but this process was independent of natural selection Problems to Resolve: At the heart was the question of whether Mendelian genetics and Mutation could be reconciled with mechanisms of Natural Selection. A second issue was whether the broad-scale changes (macroevolution) seen by palaeontologists could be explained by changes seen in local populations (microevolution). Problem caused by: Binary thinking (Black or White thinking): it s this or that if I m right, you must be wrong à When in fact the two or more factors might interact Inability to see overarching mechanism that could explain a wide range of phenomena: How could your Hardy-Weinberg (Mendel) explain the inheritance of 5.1 cm, 5.5 cm beak length (continuous characters)? à When in fact, one principle might govern and explain the different patterns Title goes here 3

4 Genetic Drift A concept as important as Natural Selection But, not as prominent on people s minds 1872 Gulick: Neutral theory (Genetic Drift) 1921 A.C. Hagedoorn produced data to support Neutral Theory Genetic Drift The Modern Synthesis 1930s ~ 1940s Also called the Synthesis of Evolution and Genetics The synthesis of population genetics (role of mutation, selection, genetic drift), paleontology, systematics Darwin and Mendel Reconciled The Modern Synthesis 1930s ~ 1940s Also called the Synthesis of Evolution and Genetics Among the Greatest Scientific Revolutions of the Century Three of the "architects" of the evolutionary synthesis: G. Ledyard Stebbins, Jr., George Gaylord Simpson, Theodosius Dobzhansky Photograph from Smocovitis, V. B G. Ledyard Stebbins, Jr. and the evolutionary synthesis ( ). American Journal of Botany 84: Some Key Tenets of the Modern Synthesis Populations are the units of Evolution The Evolutionary Synthesis was important because many scientists from different fields convened to discuss the evolutionary mechanisms and clear up confusion and inconsistencies Mendel vs Darwin: continuous traits are also coded by particulate genes, but many genes Mutation vs Selection: Mutations are sources of genetic variation upon which Selection acts Natural Selection and Mutation are not the only evolutionary forces. Examples: Genetic Drift, Recombination Microevolutionary processes, such as Drift, Selection, Mutation, lead to Macroevolutionary changes Title goes here 4

5 Some Tenets of the Evolutionary Synthesis The phenotype is different from the genotype Acquired characters (phenotypic plasticity) are not inherited Traits are inherited via genes, and they do not blend with other genes (Darwin was wrong about this one) Genes mutate, resulting in different alleles Evolution occurs at the population level, due to a change in proportions of individuals with different genotypes Changes in proportion in a population could occur via random genetic drift (Sewall Wright) or Natural Selection the rate of mutation is usually too low to cause large changes in proportions Even very weak natural selection could cause substantial changes over a longer time scale Mutations generate the genetic variation upon which natural selection acts Microevolutionary processes lead to Macroevolutionary changes (speciation) All organisms on the planet are related to one another in a great tree of life, and have diverged by branching from common ancestors Gaps in the fossil record are likely due to incompleteness of the fossil record. Gradual changes seen in many parts of the fossil record suggest gradual changes over time Mutation vs Selection and Reconciling Mendel and Darwin Mutation vs Selection And Reconciling Mendel and Darwin continuous and discrete traits could follow the same principles of inheritance (Mendel), just that continuous traits are coded by many genes (loci) If there are many genes (loci) coding for a trait, rather than one, the offspring look intermediate between the parents (looks like blending inheritance ) BUT, the SAME Mendelian patterns of inheritance apply for multi-locus traits, it s just that you don t see the particulate inheritance of each gene in the offspring, but the average effect across all the genes affecting the trait How do you deal with multi-locus quantitative traits? (2 nd point below) Hardy Weinberg: multiple alleles at a single locus: 3 alleles: (p + q + r) 2 which expands to... p 2 + 2pq + q 2 + 2pr + 2qr + r 2 =1.0 4 alleles: (p + q + r + s) 2 Hardy Weinberg: multiple loci HW principle still applies to each locus independently Need to use principles of Quantitative Genetics to examine effects of multiple loci The Population Geneticists Fisher vs Wright JBS Haldane Sewall Wright Both appreciated the importance of Natural Selection AND Genetic Drift But they argued about the relative importance Mathematical theory of population genetics showed that mutation and selection TOGETHER cause adaptive evolution: RA Fisher Mutation is NOT an alternative to Natural Selection, but the raw material upon which natural selection acts. Title goes here 5

6 Ronald Aylmer Fisher ( ) Ronald Aylmer Fisher ( ) Natural selection occurs in large populations Many genes are involved Background in math, physics, astronomy, and genetics Made key contributions to the field of Statistics Mutations are the main substrate for selection Other Contributions: Adding mathematical rigor into the theory of selection Elegant synthesis of Mendelian inheritance into the Theory of Selection Important developments in Statistics (ANOVA) Sewall Wright ( ) Sewall Wright ( ) Heavily influenced by examples from agriculture Worked for the US Dept of Agriculture: breeding in guinea pigs and cattle Became a professor at UW-Madison in Genetics Inbreeding and Genetic Drift are important for creating new gene interactions These new gene interactions (epistasis caused by new recombinations) are the main substrate for selection The Population Geneticists Reconciling Microevolutionary Mechanisms and Macroevolutionary processes If you want to read more about this topic, this book is a good read Title goes here 6

7 Ernst Mayr Microevolution à Macroevolution Ernst Mayr George Gaylord Simpson G. Ledyard Stebbins Bernhard Rensch and others George Gaylord Simpson Microevolutionary processes within species account for macroevolution among species That is, mutation, recombination, natural selection, and other processes that act within species (microevolution) are the SAME mechanisms that account for the origin of new species and major long term evolution (macroevolution) James F. Crow ( ) University of Wisconsin, Madison His work has touched on nearly every area of evolutionary genetics -will discuss some of his contributions in Lecture on Mutations Professor James Crow Lecture: Selection on Quantitative Traits (multi-locus traits): video.wpt.org/video/ / Moral of the Story Scientists from different fields should talk to each other Should avoid binary thinking (this vs. that, right vs. wrong), as different mechanisms might work together in an integrated fashion We are often biased by what we study (example of continuous vs. discrete traits) After the Evolutionary Synthesis The Importance of Natural Selection vs Genetic Drift Ongoing debate after the Evolutionary Synthesis Title goes here 7

8 Even after the synthesis the relative importance of Natural Selection and Genetic Drift was debated During the Evolutionary Synthesis, Sewall Wright focused more on importance of Genetic Drift, whereas Fisher focused on Natural Selection Shortly after the Evolutionary Synthesis many focused on selection to the point of assuming that most phenotypes were the result of Natural Selection Emphasis on Genetic Drift resurged in the 1970s, 80s with Kimura s Neutral Theory Then in the 2000s and 2010s interest in Selection increased with the ability to detect signatures of Natural Selection in genome sequence data Motoo Kimura ( ) The Neutral Theory of Molecular Evolution Classic Paper: Kimura, Motoo Evolutionary rate at the molecular level. Nature. 217: Classic Book: Kimura, Motoo (1983). The neutral theory of molecular evolution. Cambridge University Press. The Neutral Theory of Molecular Evolution (Lecture #6) The Neutral theory posits that the vast majority of evolutionary change at the molecular level is caused by random genetic drift rather than natural selection. Motoo Kimura Neutral theory is not incompatible with Darwin's theory of evolution by natural selection: adaptive changes are acknowledged as present and important, but hypothesized to be a small minority evolutionary change. Recent tests of selection have found that in many cases evolution is not neutral, even in non-coding regions of the genome. While the Evolutionary Synthesis was a HUGE leap in the right direction, there were a few tenets that required modification (as a result of new discoveries in Genetics) Nevertheless, the neutral theory is useful as a null hypothesis, against which selection could be tested. Some Tenets of the Evolutionary Synthesis The phenotype is different from the genotype Acquired characters (phenotypic plasticity) are not inherited not always true Traits are inherited via genes, and they do not blend with other genes (Darwin was wrong about this one) Genes mutate, resulting in different alleles Evolution occurs at the population level, due to a change in proportions of individuals with different genotypes Changes in proportion in a population could occur via random genetic drift (Sewall Wright) or Natural Selection the rate of mutation is usually too low to cause large changes in proportions Even very weak natural selection could cause substantial changes over a longer time scale Mutations generate the genetic variation upon which natural selection acts Microevolutionary processes lead to Macroevolutionary changes (speciation) All organisms on the planet are related to one another in a great tree of life, and have diverged by branching from common ancestors Gaps in the fossil record are likely due to incompleteness of the fossil record. Gradual changes seen in many parts of the fossil record suggest gradual changes over time not always true Completing the Synthesis Advances in Genetics Epigenetic Inheritance (Lecture #9) Some genetic changes could lead to radical changes in phenotype (Lecture #7) Polyploidization seen often in plants Changes in developmental genes Regulatory Evolution Transposons Title goes here 8

9 The role of Epigenetics (Lecture #9) Lamarck Revisited Lamarck was incorrect in thinking that the inheritance of acquired characters is the main mechanism of evolution However, we do now know that the inheritance of acquired characters does happen sometimes, through the inheritance of epigenetic modifications Evolution at the Molecular Genetic Level Which types of mutations predominate and contribute to adaptations more often? Structural vs Regulatory? Is phenotypic evolution occurring predominantly at the level of gene products (e.g. proteins) or at the level of gene regulation (e.g. transcription, RNA processing, translation, etc.)? cis-regulation vs trans-regulation? Is regulatory evolution occurring predominantly at the level of cis-regulatory elements (e.g. promoter, enhancers) or at the level of trans-acting factors (e.g. transcription factors, etc.)? More on Lectures on Molecular Evolution (Lecture #13) C.H. Waddington --his resurgence Largely dismissed during the Evolutionary Synthesisà attacked for being Lamarckian for his ideas on Genetic Assimilation Father of Developmental Biology Introduced the concept of Canalization Coined the term Epigenetics Conrad Hal Waddington Interested in the interplay between phenotypic plasticity (response to stress) and selectionà Genetic Assimilation Why did Waddington become popular starting in the 1990 s? Evo-Devo: Evolution of Development as playing an important role in the evolution of phenotypes Evolution of developmental program could cause radical phenotypic change The idea of evolution of canalization and decalanization of a developmental program Genetic Assimilation: stress could cause decanalization, and the phenotypes that are exposed could then be under selection à creation of Hopeful Monsters Evolution of Development (Lecture #26) How small changes in developmental genes (like Hox genes) could radically cause the evolution of body plans Role of Genomics (Lectures #15, 16) How does the whole genome evolve? How does selection act on networks of interacting genes? Will talk more about this when I get to lecture on Animal Diversity How many and which genes are involved in the formation of new species? Title goes here 9

10 Today: Genome Evolution and Systems Biology How do multiple genes interact? How do multiple genes affect a phenotype? Systems Biology: How does selection act on interacting gene regulatory networks? Evolution of Genome Architecture Questions: (1) What were the sources of confusion regarding evolutionary mechanisms prior to the Evolutionary Synthesis? (2) What was the Modern (Evolutionary) Synthesis? (3) What were the main tenets of the Evolutionary Synthesis? (4) What is the relationship between natural selection, genetic drift, mutations, and recombination? (5) What were some of the limitations of the Evolutionary Synthesis? (6) What were some key developments since the Evolutionary Synthesis? (7) What gaps remain in our understanding today? Sample Exam Questions 1. For several decades "Darwinists" and "Mendelists" battled over the mechanisms of evolution. Which of the following did NOT contribute to this particular conflict? (a) Geneticists/Evolutionary biologists did not understand that continuous and discrete traits follow the same principle of inheritance (b) Geneticists/Evolutionary biologists did not understand that natural selection acts on mutations in a population (c) Mendel worked with discrete traits, whereas Darwin worked with continuous traits, leading to differences in perspectives on inheritance (d) Darwin was unaware of the mechanism or unit of inheritance (e) Darwin was unaware of the mechanisms of Genetic Drift Sample Exam Question 2.Which of the following was NOT a tenet of the Evolutionary Synthesis? (a) Evolution occurs at the level of populations, in terms of changes in allele frequencies, rather than changes at the individual level (b) Selection could act on traits that are coded by multiple genes (c) Selection acts on genetic variation in traits that are caused by mutations (d) Natural Selection and Mutation are the only causes of evolutionary change (e) Microevolutionary processes within populations lead to Macroevolutionary changes among populations Answers: 1. E (Darwin did not know about Genetic Drift, but that was not a reason for the conflict between the Darwinists and Mendelists ) 2. D Title goes here 10