Unit 3- Evolution and Systematics

G-value Paradox

The concept that the number of protein coding genes in a genome does not relate to phenotypic complexity, rather it is regulatory elements that contribute to increased phenotypic complexity

Alternative Splicing

Exons of one gene can be organized in different combinations than the original DNA sequence; leads to different mRNA transcripts that can then produce different proteins.

Characteristics of Viral Genomes

1. Very diverse

2. usually haploid

3. very compact

4. some are capable of reverse transcription

Bacteriophages

Viruses that insert their genome into bacteria

Characteristics of Eukaryotic Genome

1. Small proportion is actually protein coding

2. Mostly transposable elements and non-coding regions; contains introns and regulatory sequences.

Conservative Transposons

simply ”cut” an original sequence of DNA and insert it
in a new location. It is lost in the old location (cut-paste)

Characteristics of prokaryotic genomes

Single circular chromosome with few introns, high protein-coding content, and mobile genetic elements

Retrotransposons

A transposon that copies the original element first to RNA and then back to DNA via a reverse transcriptase

Why are transposable elements called selfish genetic elements?

They replicate for their benefit, can disrupt genes, affect regulation, and cause chromosomal rearrangements.

DNA transposons

moves directly as DNA from one location in the genome to another, mainly a cut and paste mechanism, leaves a “footprint”

Non-conservative transposons

leave the original copy intact and create a new copy elsewhere (copy-paste)

What is LUCA?

Last Universal Common Ancestor – the initial population that gave rise to all extant life.

Why can’t phylogenetics fully explain the origin of life?

LUCA is a phylogenetic endpoint, and other early life forms may have gone extinct without leaving traces.

Key traits of living organisms

Homeostasis, structural organization, metabolism, response to environment, growth, and reproduction.

Earliest known fossils

Cyanobacteria-like organisms dated back to ~3.5 bya

Heredity’s role in life

Life requires a blueprint for reproduction; variation and natural selection drive evolution.

Protocells

Primitive cell-like structures formed from simple molecules under early Earth conditions.

Miller-Urey experiment

Simulated early Earth atmosphere and produced amino acids from simple gases using electric sparks; however atmosphere model was inaccurate; contamination may have occurred, but it proved abiogenesis is possible.

Evidence of an extraterrestrial origin for organic molecules

Complex molecules found in meteorites, Halley’s Comet, and Comet 67P (Rosetta mission).

Deep ocean hypothesis for life’s origin

Life may have begun at hydrothermal vents rich in chemicals and energy, facilitating complex reactions.

How do lipid membranes contribute to protocell formation?

Fatty acids can self-assemble into vesicles, which grow and divide—leading to primitive cells.

Abiogenesis

The chemical formation of life from non-living materials.

RNA world hypothesis

The hypothesis that RNA was the first genetic material, serving as both information carrier and enzyme.

Advantages of DNA

1. DNA's deoxyribose sugar is less reactive.

2. DNA's double strands protect genetic material and allow for damage repair during replication.

3. DNA replication is more efficient, has lower mutation rates, and allows for larger genomes.

Natural selection favors…

traits that increase reproductive success, regardless of complexity.

Minimal gene set approach

Studying the smallest number of genes necessary for life by comparing bacterial genomes.

Phospholipids influence on protocell growth

They stabilize vesicles, allowing for faster growth, larger protocells, and efficient division.

Mercier and co. discovery about lipid membranes

Adding fatty acids to Bacillus subtilis can reshape the cell, leading to buckling and division.

Limitations of the RNA World Hypothesis

RNA is unstable, has limited enzymatic function, and is difficult to test experimentally.

Structural advantages of DNA over RNA

More stable information carrier. Less reactive deoxyribose sugar. Double-stranded structure enables proofreading and repair.

Horizontal Gene Transfer

the movement of genetic material between organisms that are not parent and offspring; allows genes to jump between unrelated species; would allow new combinations of molecular units, leading to more complex and integrated organisms .

HGT effect on the tree of life

It creates a web-like structure rather than a simple branching tree.

Functions commonly found in minimal gene sets

DNA/RNA metabolism, protein metabolism, energy production, and folding.

Key takeaways about the origin of life

1. Early life was simpler than today.

2. RNA likely preceded DNA.

3. Natural selection promoted complexity over time.

4. Minimal gene sets help identify essential life functions.

C-value paradox

The observation that genome size (measured in gigabases) does not correlate with organismal complexity.

Viral genomes

They rely on host cells for replication, so they carry only essential genetic information.

Prokaryotic genomes’ flexibility

They often contain mobile genetic elements like plasmids and transposons, which enable horizontal gene transfer.

Plasmids

Small, circular DNA molecules in bacteria that can carry genes for advantageous traits like antibiotic resistance.

3 methods of horizontal gene transfer (HGT)

1. Transduction

2. Transformation

3. Conjugation

Transposable elements (TEs)

DNA sequences that can move within the genome, either by a 'cut and paste' (DNA transposons) or 'copy and paste' (retrotransposons) mechanism.

Disruption of genes by transposable elements

By inserting into coding sequences or regulatory regions, they can alter protein function or gene expression.

Exon shuffling

A process where recombination between exons, facilitated by introns, leads to new gene combinations and functional diversity.

Introns in eukaryotic genomes

Introns can increase recombination probability without disrupting coding sequences, promoting genetic diversity.

Genetic hitchhiking

When neutral or harmful alleles increase in frequency because they are linked to a beneficial allele under strong selection.

Regulatory elements

They control gene expression patterns, contributing significantly to an organism's phenotypic complexity, especially during development.

Earth formation

Happened about 4.54 billion years ago from the accretion of solar nebula gases and dust.

Earliest evidence of life

About 3.5 billion years ago, approximately 1 billion years after Earth formed.

Key traits of living organisms

Homeostasis, structural organization, metabolism, response to the environment, growth and reproduction, and evolution through natural selection.

Prebiotic Soup Hypothesis

The idea that life began in a 'warm little pond' with simple chemicals, energy inputs (like lightning or UV light), and no oxygen, allowing organic molecules to form.

Life starting in space theory

Complex organic molecules, including amino acids and nucleotides, have been found on meteorites and comets (e.g., Halley's comet and Comet 67P).

Life starting in deep oceans theory

Hydrothermal vents provide heat, pressure, and abundant complex compounds that could catalyze chemical reactions leading to life.

Advantage of phospholipids in protocells

Phospholipids stabilize membranes, enabling faster growth, larger protocells, and more efficient division, giving a selective advantage.

Cell division from lipid membranes

As vesicles grow and incorporate more lipids, their surface area increases, potentially causing the membrane to buckle and divide, sharing internal contents — an early step toward cellular reproduction.

Evidence for the RNA World Hypothesis

1. RNA can act as enzymes (ribozymes).

2. DNA synthesis requires an RNA intermediate.

3. Ribosomes (protein factories) are made entirely of RNA at their core.

4. Experiments show RNA components were present on early Earth.

Major evolutionary transitions proposed by Smith & Szathmáry

1. Origin of self-replicating molecules.

2. Transition from RNA to DNA + proteins.

3. Origin of eukaryotic cells.

4. Evolution of multicellular organisms and developmental complexity.

5. Evolution of social groups and eusociality.

Natural selection and complexity

Natural selection favors traits that improve reproductive success in a given environment — many organisms remain simple because simplicity works.

Transition from RNA to DNA

The evolutionary shift where DNA became the primary genetic material, replacing RNA.

Origin of first cells

The emergence of the first cellular life forms.

Origin of eukaryotic cells

The development of complex cells with membrane-bound organelles.

Evolution of sexual reproduction

The development of reproduction involving the combination of genetic material from two parents.

Evolution of multicellular organisms

The process by which single-celled organisms evolved into complex multicellular forms.

Evolution of developmental complexity

The increase in complexity of developmental processes in organisms over time.

Evolution of individuality, groups, and eusociality

The emergence of distinct individual organisms and social structures within groups.

Three important properties of major evolutionary transitions

1. Individual units give up independent reproduction.

2. Groups gain efficiency through economies of scale and specialization.

3. Groups improve information processing.

Economy of scale concept

A group can perform tasks more efficiently than individuals, e.g., social insects hunting larger prey.

Heterochrony

Evolutionary change in the timing or rate of developmental events, leading to changes in size and shape of organisms compared to their ancestors; when certain parts of an organism develop faster, slower, earlier, or later than they used to and this change affects the final form of the organism

Recapitulation

Somatic traits develop earlier relative to reproductive traits.

Paedomorphosis

Somatic traits develop later relative to reproductive traits.

Specialization and efficiency

Division of labor increases efficiency, e.g., cell specialization in multicellular organisms.

Cooperation in evolutionary transitions

Coordinated groups outcompete individuals who cheat, promoting stability in group living.

Genetic imprinting

A phenomenon where some genes only express maternal or paternal alleles, making asexual reproduction impossible in mammals.

Parthenogenesis

A form of asexual reproduction where embryos develop without fertilization, seen in plants, fish, lizards, and snakes but not in mammals.

Age of eukaryotic cells

Microfossils suggest ~2 billion years, while phylogenetic estimates suggest ~1 billion years.

Endosymbiotic theory

The idea that mitochondria and chloroplasts originated from symbiotic relationships with bacteria.

Evidence of endosymbiotic theory

Mitochondria and chloroplasts have two membranes, their own single-copy genomes, and DNA linking them to proteobacteria (mitochondria) and cyanobacteria (chloroplasts).

Migration of organellar genes to the nucleus

Over time, genes originally exclusive to mitochondria and chloroplasts were transferred to the host cell's nuclear genome.

Why multicellularity evolved independently many times

Because it provides advantages like economy of scale, specialization, and improved information processing.

Endosymbiosis in eukaryotic evolution

Allows multiple organisms to merge and form complex cells with specialized organelles.

Two main routes to multicellularity

1. Staying together: Cells divide but remain attached, genetically identical.

2. Coming together: Free-living cells join into a multicellular group, leading to genetic diversity and potential reproductive conflict.

Benefits of multicellularity

1. Communication: Cells can follow stimuli like light and food.

2. Protection: Slime layer protects against predators.

3. Efficiency: Specialization of cells increases efficiency and speed.

4. Economy of scale: Better surface area-to-volume ratio.

How individuality evolves in multicellular organisms

Fitness transfers from individual cells to the whole organism, requiring: Germ cells for reproduction, Somatic cells for maintenance and growth, and Loss of totipotency in somatic cells.

Definition of a group in evolutionary biology

A set of conspecific individuals (same species) who affect each other's fitness.

Benefits of group living

1. Foraging: Better success and efficiency (e.g., fish hunting, chimpanzee hunting groups).

2. Protection: Predator detection and avoidance.

3. Reproduction: More mates, shared care of young.

Costs of group living

1. Resource competition

2. Cheating behavior

3. Parasites and pathogens

Evo-Devo

The study of how developmental processes evolve and influence adaptations, linking gene expression to phenotypic changes; the study of how organisms develop throughout their lifetimes and how this is associated with their evolution.

Categories of heterochrony

1. Recapitulation

2. Paedomorphosis

Types of paedomorphosis

1. Progenesis: Development stops early because sexual maturity happens sooner

2. Neoteny: Development slows down, so the body matures more slowly than sexual maturity.

Totipotent cells

Cells in early development that can differentiate into any cell type in the body.

Homeotic genes

They determine the identity and positioning of anatomical structures during development.

Hox genes

A type of homeotic gene found in all animals, responsible for anterior-to-posterior body structure positioning.

Collinearity in Hox genes

The order of Hox genes on the chromosome corresponds to the relative position of the body parts they regulate.

Conservation of Hox genes

The homeobox domain (180-base-pair region) is highly conserved across animal species, indicating its evolutionary importance.

MADS- box genes

homeotic genes for plants, involved in positioning of cells

Regulatory enhancers

They act as switches that turn genes on and off, affecting expression levels, and influencing the level and location of gene expression.

How regulatory elements produce differences between species

Differences in regulatory enhancers, even with similar genetic sequences, lead to major phenotypic differences (e.g., humans and chimps share ~98% DNA similarity but differ phenotypically due to regulatory elements).

DNA methylation in gene expression

It affects the activity of regulatory elements, influencing the timing and level of gene expression.

Cis-regulatory elements

Noncoding stretches of DNA that control the spatial and temporal expression of nearby genes.

Gene duplications’ role in development

Increases complexity and the evolution of new traits.

Paralogs

Duplicated genes that are maintained and may take on new or specialized functions.

Fates of a duplicated gene

Gene loss: The new copy may be eliminated or become a pseudogene.

Sub-functionalization: Both copies divide the original gene's functions.

Neofunctionalization: One copy evolves a completely new function.