history - university of wisconsin–madison · bird clutch, presence/absence of human widow’s...

Carol Eunmi Lee 9/11/19

Title goes here 1

Dr. Carol Eunmi LeeUniversity of Wisconsin, Madison

History of Evolutionary Thought:

The Grand Evolutionary SynthesisConsidered one of the most important Biological Revolutions of the Century

(1) The Sources of Confusion

(2) Reconciling Mendel and Darwin

(3) The Main Tenets of the Evolutionary

Synthesis

(4) Key Developments since the Synthesis

(5) Gaps in our Understanding Today

Today’s OUTLINE:

Charles Darwin (1809-1882)

Last time we discussed Darwin’s contributions to evolutionary thinking

Darwin’s contribution:

“Population Speciation as a result of Natural Selection”

■ 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

Question:■ What body of knowledge

provided Darwinian theory with the concept of “genes” and inheritance?


Title goes here 2

■ 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)

Mendel’s work held part of the key to what was missing in Darwin’s Theory

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

■ These rediscoveries 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 Mendelian expectations are realized in nature

■ Did the Darwinists accept Mendelian Genetics?

■ Why or Why Not?

PROBLEMS!

BUT… Mendel and Darwin’s ideas seemed Incompatible

■ 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?


Title goes here 3

Selection vs Mutations

■ Mutations discovered after 1900

Q: If mutations are arising, why need selection... … if things are just mutating?

Controversy between Mutationists vs DarwinistsMutationists (+ 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

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

Discrete vs Quantitative Traits■ Darwin was unable to clearly see the pattern of

inheritance because he studied quantitative variation

•• 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

Type

Example: human height encoded by ~423 genes:http://www.nature.com/ng/journal/v46/n11/full/ng.3097.html

■ 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 Darwinist 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

■ New species originated when they mutated from pre-existing species, but this process was independent of natural selection

Proponents of the Mutationist/Mendelist Theory


Title goes here 4

Controversy between Mutationists vs Darwinists

Controversy persisted for ~30 years up till the 1930s, during which little progress was made

Problems to Resolve:

■ At the heart was the question of whether Mendeliangenetics 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)?”

àWhen in fact, one principle might govern and explain the different patterns

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 Synthesis1930s ~ 1940s

Also called the “Synthesis of Evolution and Genetics”The synthesis of population genetics(integrate the roles of mutation, selection, genetic drift, paleontology, systematics)

Darwin and Mendel Reconciled

The Modern Synthesis1930s ~ 1940s

Also called the “Synthesis of Evolution and Genetics”

Among the Greatest Scientific Revolutions of the Century


Title goes here 5

Three of the "architects" of the evolutionary synthesis:G. Ledyard Stebbins, Jr., George Gaylord Simpson, Theodosius Dobzhansky

Photograph from Smocovitis, V. B. 1997. G. Ledyard Stebbins, Jr. and the evolutionary synthesis (1924-1950). American Journal of Botany 84: 1625-1637.

The Evolutionary Synthesis was important because many scientists from different fields convened to discuss the evolutionary mechanisms and clear up confusion and inconsistencies

Some Key Tenets of the Modern Synthesis■ Populations are the units of Evolution

■ 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

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

■ With which of these tenets do you agree?

■ With which do you not agree?

Mutation vs Selectionand Reconciling Mendel and Darwin


Title goes here 6

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? (2nd point below)

■ Hardy Weinberg: multiple alleles at a single locus:◆ 3 alleles: (p + q + r)2 which expands to...

p2 + 2pq + q2 + 2pr + 2qr + r2 =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

JBS HaldaneSewall Wright

RA Fisher

The Population Geneticists

Mathematical theory of population genetics showed that mutation and selection TOGETHER cause adaptive evolution:

Mutation is NOT an alternative to Natural Selection, but the raw material upon which natural selection acts.

Fisher vs WrightBoth appreciated the importance of Natural Selection AND Genetic DriftBut they argued about the relative importance

Background in math, physics, astronomy, and genetics

Made key contributions to the field of Statistics

Developed the Foundations for the mathematics of Natural Selection

Ronald Aylmer Fisher (1890-1962)

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)

Ronald Aylmer Fisher (1890-1962)• Natural selection occurs in large populations

• Many genes are involved

• Mutations are the main substrate for selection


Title goes here 7

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

Sewall Wright (1889-1988)

• 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

I’ll talk a lot about Sewall Wright in the lecture on Genetic Drift

Sewall Wright (1889-1988)

The Population Geneticists

If you want to read more about this topic, this book is a good read

Reconciling Microevolutionary Mechanisms and Macroevolutionary processes

Microevolution à Macroevolution

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)

Ernst Mayr

Ernst MayrGeorge Gaylord SimpsonG. Ledyard StebbinsBernhard Renschand others

George Gaylord Simpson

http://www.genetics.wisc.edu/CATG/crow/index.html

James F. Crow (1916-2012)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


Title goes here 8

video.wpt.org/video/1811393836/

Professor James Crow Lecture:

Selection on Quantitative Traits (multi-locus traits):

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

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 RA 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 dataàmuch of the genome is under selection

Motoo Kimura (1924-1994)

The Neutral Theory of Molecular Evolution

Classic Paper: Kimura, Motoo. 1968. Evolutionary rate at the molecular level. Nature. 217: 624–626.

Classic Book: Kimura, Motoo (1983). The neutral theory of molecular evolution. Cambridge University Press.

http://video.wpt.org/video/1811393836/


Title goes here 9

The Neutral Theory of Molecular Evolution (Lecture #6)

• 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.

• Purifying selection (negative selection) could still be acting to remove deleterious mutations from the genome. But, the idea here is that most of the genetic variation within and between populations is due to neutral variation.

• **Ongoing debate on the extent to which variation across the genome is caused by genetic drift vs. natural selection

Motoo Kimura

• 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.

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)

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

■ Epigenetic Inheritance

■ Some genetic changes could lead to radical changes in phenotype◆ Polyploidization, through polyploid hybridization or

Whole Genome Duplication◆ Regulatory Evolution (e.g. transcription factor

evolution, as TFs regulate many genes)à often leads to radical evolution of development

◆ Transposons

Advances in Genetics

The role of Epigenetics■ Lamarck Revisited

■ Lamarck was incorrect in thinking that the inheritance of acquired characters is the main mechanism of evolution

■ However, we now know that the inheritance of acquired characters does happen sometimes, through the inheritance of epigenetic modifications (Epigenetic Inheritance)

■ Yet, the extent to which epigenetic inheritance occurs is still not known and controversial (experimentally difficult to confirm), especially in animals

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”


Title goes here 10

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 decanalization 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

■ Will talk more about this when I get to lecture on Animal Diversity

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

Role of Genomics(Lectures #15, 16)

■ How do whole genomes evolve?

■ How does selection act on networks of interacting genes?

■ How many and which genes are involved in the formation of new species?

Today: Genome Evolution and Systems Biology

■ How do multiple genes interact?■ How do multiple genes affect a phenotype?(questions about the “genotype-phenotype map”)

■ 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 leading up 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?


Title goes here 11

1. For several decades "Darwinists" and "Mendelists" battled over the mechanisms of evolution. Which of the following did NOTcontribute 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 Questions Sample Exam Question2.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

history - university of wisconsin–madison · bird clutch, presence/absence of human widow’s...

Documents