4/10-4/24 Lecture Notes

What are the two central problems of development in multicellular organisms?

(1) How does a single cell make an adult body? (2) How does an adult body make offspring?

What is the genotype-phenotype map?

It's the process that maps genetic information (genotype) to the physical form (phenotype).

Why is the evolution of phenotypes really the evolution of development?

Because phenotypes are produced through developmental processes.

What is heterochrony?

Evolutionary change in the timing and rate of developmental events (e.g., neoteny).

Define pleiotropy.

One gene affects multiple traits.

Define epistasis.

When the effect of one gene is modified by one or more other genes.

What is antagonistic pleiotropy?

A gene has multiple effects that may be beneficial for one function but harmful for another.

How does gene duplication contribute to complexity?

It allows one gene copy to maintain function while the other diversifies or gains new functions.

What are the three possible outcomes after gene duplication?

(1) Subfunctionalization, (2) Neofunctionalization, (3) Pseudogenization.

What is subfunctionalization?

Duplicate genes divide the original functions between them.

What is neofunctionalization?

One gene copy acquires a new function.

What is canalization?

The ability of a genotype to produce the same phenotype regardless of environmental variability.

What is modularity in development?

Traits grouped into semi-independent modules, allowing easier evolutionary changes.

What role do Hox genes play in development?

They control anterior-posterior body patterning and segment identity.

What is an evolutionary transition in individuality (ETI)?

A transition from a group of cooperating individuals into a new, higher-level evolutionary individual.

Give three examples of major ETIs.

(1) RNA replicators to protocell, (2) Prokaryotes to eukaryotic cells, (3) Cells to multicellular organisms.

What is fitness decoupling?

Group-level fitness becomes independent of the average fitness of lower-level units.

What are key criteria for individuality?

Indivisibility, genetic homogeneity, spatial/temporal boundaries, physiological integration, and division of labor.

What’s the role of germ-soma differentiation in ETIs?

It enables division of labor and specialization in reproduction vs. somatic maintenance.

What is the volvocine algae clade used to study?

Gradual evolution of multicellular individuality (e.g., Gonium to Volvox).

What is meant by 'reorganization of fitness'?

Fitness shifts from individuals to the group level as specialization evolves.

What mechanisms support ETIs?

Cooperation, conflict mediation, co-option of life-history genes, and specialization.

What’s an example of a species with partial individuality?

Gonium—cells can survive alone and group fitness equals average cell fitness.

What is the significance of Volvox in ETI studies?

It exhibits complete fitness decoupling and full germ-soma differentiation.

What is the hierarchical structure of life?

Nested levels of organization: genes → cells → multicellular organisms → social groups.

What is the paradox of sex?

Despite high costs, sex is common. Why? What are its evolutionary benefits?

List three major costs of sexual reproduction.

(1) 2-fold cost of males, (2) Breaks apart beneficial gene combinations, (3) Energy for mating.

What is recombination?

The process of mixing genetic material through crossing-over or DNA exchange.

What is linkage disequilibrium (LD)?

Non-random association of alleles at different loci.

Why does sex matter more when LD ≠ 0?

Because recombination can reshuffle alleles more effectively under LD.

What is Muller’s Ratchet?

Asexual populations accumulate deleterious mutations over time.

What is the Fisher-Muller hypothesis?

Sex accelerates adaptation by combining beneficial mutations.

What is the Red Queen hypothesis?

Sex allows hosts to keep up in evolutionary arms races with parasites.

How did meiosis evolve?

Through gene duplication of prokaryotic DNA repair genes (e.g., RecA → Rad51, Dmc1).

What is amphimixis?

Sexual reproduction involving meiosis and fusion of gametes from two parents.

How does sex relate to DNA repair?

Meiotic recombination evolved to repair double-strand DNA damage.

What is the DSBR model?

The double-strand break repair model of meiotic recombination.

What is the origin of meiosis genes like Spo11 and Dmc1?

They evolved by duplication from DNA repair genes in prokaryotes.

What is the 'immortality of life' concept in this context?

Sex preserves the continuity and integrity of life by preventing the accumulation of mutations.

What are the two main problems of development in multicellular organisms?

(1) How a single cell makes an adult body; (2) How an adult makes offspring.

What does the 'genotype-phenotype map' represent?

It describes how genetic information results in adult phenotypes through development.

What is pleiotropy?

When one gene affects multiple traits.

What is antagonistic pleiotropy?

When a gene has multiple effects, some beneficial and some harmful.

How can evolution escape constraints of pleiotropy?

Through gene duplication, allowing new or divided functions.

Define subfunctionalization.

A duplicated gene pair splits the tasks of the original gene.

Define neofunctionalization.

One duplicated gene evolves a new function.

What are orthologous genes?

Genes in different species that evolved from a common ancestral gene via speciation.

What are paralogous genes?

Genes within a species that result from duplication events.

What role do Hox genes play?

They determine the identity and position of body segments during development.

What does colinearity in Hox genes mean?

Gene order on the chromosome matches the body regions they regulate.

What is the role of enhancers in gene expression?

Enhancers regulate when, where, and how much a gene is expressed.

How can gene duplication contribute to evolutionary complexity?

It creates new genetic material for evolution to modify, enabling new traits and structures.

What is modularity in development?

The organization of development into units (modules) that can change independently.

What are the two main developmental questions in EvoDevo?

(1) How does a single cell make an adult body? (2) How does an adult make offspring?

How are phenotypes and development related in evolution?

Phenotypes arise through development, so evolving phenotypes means evolving development.

What phrase summarizes EvoDevo compared to Darwin's?

"Arrival of the fittest" (EvoDevo) vs. "Survival of the fittest" (Darwin).

What does the genotype-phenotype map represent?

It shows how genes produce the adult form via development.

What is pleiotropy?

One gene has multiple effects on different traits.

What is epistasis?

Interaction between genes where one gene affects another’s expression.

What is canalization?

Stability of development despite genetic or environmental changes.

What is modularity in development?

Development organized into semi-independent units that can evolve separately.

Why did early replicators (e.g., ribozymes) exhibit pleiotropy?

Because a single molecule had to perform multiple functions.

What is antagonistic pleiotropy?

A gene that has both beneficial and harmful effects, depending on the context.

What evolutionary challenge does pleiotropy present?

It constrains the evolution of complexity.

How does gene duplication help overcome pleiotropy?

It allows functions to split, new functions to evolve, or redundant copies to become inactive.

What is subfunctionalization?

Duplicated genes divide the original functions between them.

What is neofunctionalization?

One gene copy evolves a new function after duplication.

What is pseudogenization?

One gene copy loses its function and becomes inactive.

In the genotype-phenotype map, what does each gene represent?

An axis of gene value that influences phenotype.

How does gene duplication increase complexity in the fitness landscape?

It adds new axes, increasing possible combinations and fitness peaks.

What are orthologs?

Genes in different species that originated from a common ancestral gene via speciation.

What are paralogs?

Genes that arose from duplication within the same genome.

Why do humans and chimps differ if their proteins are similar?

Differences often lie in gene regulation, not protein-coding regions.

What are cis-regulatory elements?

DNA sequences (like enhancers/silencers) that control gene expression near a gene.

What are trans-acting factors?

Proteins like transcription factors that bind DNA and regulate gene expression.

How do tissue-specific enhancers affect fruit fly pigmentation?

Gain or loss of enhancer binding sites can cause or remove pigmentation in certain tissues.

What is a homeotic mutation?

A mutation where one body part transforms into another.

What do Hox genes do?

They assign identities to body segments and control pattern formation.

What is colinearity in Hox genes?

The gene’s location on the chromosome matches its spatial effect on the body axis.

How does Hox gene modularity facilitate evolution?

Modules can be reused or rearranged without disrupting the whole organism.

What are key innovations in the evolution of complexity?

Larger body size, division of labor, spatial patterning, gene duplication, and co-option.

What does the regA gene do in Volvox?

It controls somatic cell differentiation, co-opted from a unicellular ancestor gene (rls1).

What does the Volvox case study show about complexity?

Complexity can evolve through gene duplication and regulatory gene changes from unicellular ancestors.

What is an evolutionary transition in individuality (ETI)?

A major evolutionary shift where a group of cooperating individuals becomes a new kind of evolutionary individual.

What are Darwinian properties required for individuality?

Variation, heritability, and differential fitness.

What does it mean for group fitness to be decoupled from cell fitness?

The group's success no longer depends on the average success of individual cells.

Which organism has group fitness decoupled from cell fitness—Gonium or Volvox?

Volvox.

What role does division of labor play in ETIs?

It allows specialization (e.g., soma/germ cells), increasing integration and functionality of the group.

What is fitness reorganization during an ETI?

Fitness shifts from individuals to the group, enabling group-level selection.

What criteria define individuality in multicellular organisms?

Indivisibility, genetic homogeneity/uniqueness, division of labor, group-level adaptations, and fitness decoupling.

How do volvocine algae illustrate ETIs?

They show a stepwise increase in individuality traits across species, from unicellular to fully multicellular.

What are some mechanisms of conflict mediation in ETIs?

Policing (e.g., immune system), kin selection, reciprocation, and structural barriers like germ-soma separation.

What is an example of a new evolutionary individual from ETIs?

The eukaryotic cell, which evolved from a group of bacterial and archaeal cells.

What is the key difference between Gonium and Volvox in terms of individuality?

Gonium has lower individuality and fitness coupling; Volvox has higher individuality and fitness decoupling.

Why is ETI theory important in understanding evolution?

It explains how major jumps in complexity and new evolutionary individuals arise.

What does ETI stand for in evolutionary biology?

Evolutionary Transitions in Individuality.

What is an ETI?

A major shift where a group of cooperating individuals evolves into a new kind of evolutionary individual.

Give three examples of evolutionary transitions in individuality (ETIs).

RNA replicators → Protocells; Prokaryotes → Eukaryotic cells; Unicellular organisms → Multicellular organisms.

What defines an evolutionary individual?

An integrated, indivisible whole that can reproduce and transmit heritable variation.

What are the Darwinian properties of an evolutionary individual?

Variation, heritability, and differential fitness.