Origin of Life, Evo-Devo & Phylogenetics – Exam Review

Question-and-Answer flashcards covering origin of life chemistry, RNA world, horizontal gene transfer, endosymbiosis, Evo-Devo concepts (homeotic genes, enhancers, gene duplication, neural crest), and phylogenetic principles (tree reading, homology vs analogy, synapomorphy, parsimony, distance, likelihood/Bayesian methods, bootstrapping, comparative analysis).

Why can natural selection not act on non-heritable variation?

Because only heritable (genetically based) phenotypic differences are passed to offspring, allowing differential reproductive success to shape future generations.

What does LUCA stand for?

Last Universal Common Ancestor – the most recent common ancestor of all extant life forms.

What is the phylogenetic event horizon?

A point early in life’s history beyond which phylogenetic analysis cannot reliably reconstruct relationships (e.g., before LUCA).

Which informational molecule likely preceded DNA in early life?

RNA – it could both store genetic information and catalyze reactions.

State the Prebiotic Soup Hypothesis.

Life arose gradually from inorganic molecules in Earth’s early, oxygen-free atmosphere, energized by UV light, lightning, or volcanism.

What gases did Miller & Urey use to simulate early Earth?

Methane (CH4), ammonia (NH3), hydrogen (H2), and water vapor (H2O).

Key outcome of the 1953 Miller–Urey experiment?

Spontaneous formation of amino acids under simulated early-Earth conditions.

How do hydrothermal (black smoker) vents contribute to origin-of-life scenarios?

Provide mineral-rich, high-energy environments that can drive organic synthesis and concentrate molecules.

Why is ocean dilution a problem for the prebiotic soup model?

Low concentrations of organic molecules would slow reaction rates and hinder polymer formation.

What property of lipids allows spontaneous vesicle formation?

Amphipathic nature: hydrophilic heads and hydrophobic tails self-assemble into bilayers in water.

Why do reactions occur faster on clay surfaces than in bulk solutions?

Clay adsorbs and concentrates reactants, aligning them for polymerization (e.g., nucleotide chains).

Define ‘protocell’.

A membrane-bounded vesicle containing self-replicating molecules and basic metabolism, viewed as an ancestor to true cells.

What is a ‘hypercycle’?

A network of self-replicating molecules (e.g., RNAs) that mutually enhance each other’s replication within a confined space.

List two lines of evidence that modern ribosomes are molecular fossils of the RNA world.

1) The catalytic peptidyl-transferase center is RNA (a ribozyme). 2) Many enzyme cofactors contain ribonucleotides.

Why did natural selection favor a switch from RNA to DNA genomes?

DNA’s deoxyribose lacks the 2′-OH, making it chemically more stable and less prone to mutation; proofreading DNA polymerases further reduce errors.

Define Horizontal Gene Transfer (HGT).

Movement of genetic material between unrelated organisms, not by parent-to-offspring inheritance.

Role of HGT in early evolution according to Woese.

High HGT created modular, rapidly evolving cells; as complexity increased, vertical inheritance became dominant, giving rise to the three domains.

What is a minimal gene set?

The core group of genes required for DNA/RNA metabolism, protein folding, and basic energetics—universally essential for life.

Endosymbiotic theory explains the origin of which organelles?

Mitochondria (from α-proteobacteria) and chloroplasts (from cyanobacteria).

Give one genomic piece of evidence for the bacterial origin of mitochondria.

Mitochondrial DNA is circular and most similar to α-proteobacterial genomes.

Which domain’s genes dominate eukaryotic transcription/translation machinery?

Archaeal genes (informational genes).

Current leading hypothesis for eukaryotic nucleus origin?

An archaeal host fused with/engulfed a bacterium; archaeal lineage contributed the nucleic DNA-handling machinery.

What does Evo-Devo study?

How evolutionary changes in developmental genetic programs generate new body forms.

Difference between homeotic and regulatory (enhancer/silencer) genes.

Homeotic genes specify body part identity; regulatory elements control when/where genes (including homeotics) are expressed.

Function of Hox genes in animals.

Master regulators that pattern the anterior-posterior (head-to-tail) body axis.

What phenotype results from Ubx loss in flies?

Conversion of halteres into a second pair of functional wings (four-winged fly).

Plant equivalent of animal Hox genes?

MADS-box genes – they control floral organ identity.

Define ‘homeobox’.

A conserved 180-bp DNA sequence within homeotic genes encoding a 60-aa homeodomain that binds DNA.

What is colinearity in Hox clusters?

Chromosomal order of Hox genes matches their spatial expression along the body axis.

Deep homology meaning?

Distantly related organisms share conserved developmental genes; small regulatory changes create large morphological differences.

How can multiple independent enhancers affect one gene’s expression?

Each enhancer can drive expression in different tissues or developmental stages, allowing modular evolutionary changes.

Most common mechanisms producing gene duplicates.

Unequal crossing-over and retrotransposition.

Name three evolutionary fates of duplicated genes.

1) Non-functionalization (pseudogene) 2) Subfunctionalization (division of labor) 3) Neofunctionalization (new function).

What are paralogs?

Duplicated homologous genes within the same genome that can diverge in function.

Why did Hox clusters expand during animal evolution?

Extra copies allowed greater regulatory complexity, enabling more elaborate body plans.

Example of subfunctionalization in plants.

OEP16 gene duplication: one copy specialized for seeds, the other for pollen.

What are neural crest cells?

Multipotent, migratory embryonic stem cells in vertebrates that give rise to diverse tissues (e.g., cartilage, neurons, pigment cells).

Duck–quail beak transplant experiments showed what?

Neural crest cells carry species-specific instructions for beak morphology, confirming their developmental role in vertebrate diversity.

Define phylogeny.

Evolutionary history and relationships among species, often visualized as a branching tree.

Why shouldn’t tip proximity be used to infer relatedness on a tree?

Branching order (shared ancestors), not horizontal distance, indicates evolutionary relationships.

What is a polytomy?

An unresolved node with >2 descendant lineages, indicating uncertainty about branching order.

Purpose of an outgroup in phylogenetic analysis.

Roots the tree and helps determine which character states are ancestral versus derived.

Define monophyletic clade.

A group containing a common ancestor and all its descendants.

Difference between paraphyletic and polyphyletic groups.

Paraphyletic: ancestor + some but not all descendants; Polyphyletic: taxa lacking their most recent common ancestor, grouped by convergent traits.

Cladogram vs phylogram vs chronogram.

Cladogram: topology only; Phylogram: branch lengths = amount of change; Chronogram: branch lengths scaled to time.

Homology vs analogy definitions.

Homology: similarity due to shared ancestry; Analogy: similarity due to convergent evolution.

Give an example of convergent evolution producing analogous traits.

Wings in bats, birds, and insects (flight evolved independently).

Vestigial trait meaning and evolutionary significance.

A reduced, nonfunctional structure inherited from ancestors, supporting common descent (e.g., human plica semilunaris).

What is a synapomorphy?

A shared derived character that diagnoses a clade.

Symplesiomorphy definition.

A shared ancestral character present in multiple taxa but not informative for defining a clade.

Autapomorphy definition.

A derived character unique to a single lineage.

Define homoplasy.

Similarity in traits due to independent evolution (convergence or reversal), not shared ancestry.

State Dollo’s Law.

Complex traits, once lost, are unlikely to re-evolve in the exact same form; apparent reversals are usually new solutions (homoplasy).

Principle of parsimony in tree building.

Prefer the phylogeny requiring the fewest evolutionary changes.

Why can parsimony mislead when evolutionary rates differ among lineages?

Fast-evolving taxa accumulate more changes and may appear distantly related even when they are not (long-branch attraction).

What do distance methods use to build trees?

Overall similarity (e.g., number of DNA or morphological differences) converted into pairwise distances.

Main drawback of distance-based trees.

They may cluster taxa by convergent similarity rather than true shared ancestry.

Maximum likelihood vs Bayesian phylogenetics – key difference.

ML finds the single tree with highest likelihood given a model; Bayesian samples many trees, weighting them by posterior probability.

What is the Jukes–Cantor model?

A simple DNA substitution model assuming equal base frequencies and equal rates for all changes.

How does the Kimura 2-parameter model improve on Jukes–Cantor?

It distinguishes between transition and transversion rates, making it more realistic.

Define ‘nuisance parameters’ in phylogenetics.

Model parameters (e.g., substitution rates) that must be estimated to infer the tree but are not of primary interest.

What does bootstrap support measure?

How often a clade appears in phylogenetic trees built from resampled datasets; higher % indicates stronger support.

Why can’t parsimony trees yield odds-ratio tests for clades?

They do not compute likelihood scores needed for statistical comparison of alternative hypotheses.

Comparative method purpose.

Tests for correlated trait evolution across species by accounting for shared ancestry.

What is an independent contrast?

A data point representing the difference in trait values between sister lineages, used to control for phylogenetic non-independence.

Correlation of independent contrasts indicates what?

Parallel evolutionary changes likely driven by natural selection, not just shared ancestry.

Formula: How many rooted trees can be produced from an unrooted tree with k species?

(2k – 3) rooted trees (root can be placed on any branch of the unrooted tree).

Why did Ebola sequences from Mali show fewer amino-acid than nucleotide differences?

Many nucleotide mutations were silent (synonymous), not altering encoded amino acids.

Horizontal Gene Transfer’s effect on early vs modern life.

Early life: rampant HGT promoted rapid innovation; Modern life: reduced HGT, vertical inheritance dominates within the three domains.