1-5 The Evolutionary Foundations

Mutation, recombination and gene transfer create variation; selection and drift change its frequency.

• Evolution — change in the genetic composition of a population across generations
• Sources of variation — substitutions, insertions, deletions, copy-number and chromosomal changes; meiotic recombination; horizontal gene transfer in bacteria and archaea
• Not every change alters protein — synonymous substitutions, regulatory-region changes, and amino-acid changes with little functional effect
• Natural selection — requires heritable trait variation linked to differences in reproductive success
• Genetic drift — random change in allele frequency in finite populations, independent of fitness
• Selection model — p′ = p(1+s)/(1+ps); with p = 0.20 and s = 0.10, p′ ≈ 0.216, a gain of about 0.016 per generation
• Caution — mutations do not arise in anticipation of future benefit

Experiments show that organic molecules can form abiotically; they do not show how replication began.

• Chemical evolution — formation of organic molecules and increasingly complex reaction systems without life, some of which may have acquired replication and selection
• Miller–Urey (1953) — circulating water and simple gases with electrical discharge produced amino acids and other organics
• What it proves — organic synthesis is possible under abiotic conditions
• What it does not prove — the exact composition of the early atmosphere, or that the same path occurred on early Earth
• Compartments — amphiphilic molecules form micelles and vesicles that concentrate reactants and separate inside from outside
• But — a membrane alone does not create heredity or metabolism; replication, energy supply, growth and division must be coupled

The RNA world hypothesis rests on one molecule doing two jobs: storing information and catalysing reactions.

• Division of labour today — DNA stores, proteins catalyse, RNA transmits and regulates
• Hypothesis — at some stage RNA, or a similar polymer, both stored information and catalysed replication chemistry
• Ribozymes — Cech’s self-splicing RNA and Altman’s RNase P showed that RNA can catalyse; Nobel Prize in Chemistry, 1989
• Ribosome — the peptidyl transferase centre is ribosomal RNA, a surviving RNA catalyst
• Unresolved problems — sufficient activated nucleotides, stable long chains, control of copying errors, resistance to hydrolysis, and coupling to membranes and energy metabolism
• Open alternatives — earlier polymers, short peptides or mineral catalysts may have preceded RNA

Fossils and geochemical signals date early life; molecular clocks and LUCA answer a different question.

• Earth — formed about 4.54 billion years ago
• Strong evidence — stromatolites and microbial traces around 3.5 billion years ago
• Older claims — reports near 3.7 billion years remain debated because abiotic structures and alteration must be excluded
• Converging evidence — stromatolite layering, microfossil morphology, carbon isotope fractionation, organic composition and geological context
• Molecular clock — estimates divergence times from sequence differences, evolutionary rate and fossil calibration; rates vary and horizontal transfer complicates inference
• LUCA — the last universal common ancestor, not the first cell; a 2024 phylogenomic study estimated about 4.2 billion years ago (range ≈ 4.09–4.33), one model rather than a settled date
• Textbook statement — life was present at least 3.5 billion years ago

Chemolithotrophy and chemiosmosis offer plausible energy strategies for early life.

• Phototrophy — photons raise electrons to higher energy states and drive energy-conserving reactions
• Chemotrophy — free energy released by oxidation–reduction reactions drives ATP synthesis
• Chemolithotrophs — use inorganic electron donors such as H₂, H₂S, Fe²⁺ and NH₃
• Methanogenesis — 4H₂ + CO₂ → CH₄ + 2H₂O in specific archaeal lineages, not all archaea
• Hydrothermal systems — supply mineral catalysts, reducing species, pH and temperature gradients
• Chemiosmosis — proton-motive force combining membrane potential and pH gradient is used by many organisms today, suggesting an ancient origin
• What is claim vs evidence — "used inorganic fuels" is a well-supported inference, not a demonstrated reconstruction of the first cell

An archaeal host plus a bacterial symbiont explains the chimeric eukaryotic cell.

• Host lineage — eukaryotes are phylogenetically nested within Archaea, close to the Asgard lineages
• Mitochondria — derived from an alphaproteobacterium taken up as a symbiont
• Evidence — own genomes, division by fission, bacterial-type ribosomes and genes, phylogenetic signals in organellar proteins
• Gene transfer — many organellar proteins are now encoded in the nucleus, synthesised in the cytoplasm and imported
• Chloroplasts — primary endosymbiosis with a cyanobacterium; secondary symbiosis occurred in some lineages
• Still debated — the timing of the nuclear envelope, cytoskeleton and endomembrane system, and the exact order of mitochondrial acquisition

Sequence similarity suggests homology; a phylogenetic tree is a statistical hypothesis, not a fact.

• Shared molecules — DNA, RNA, proteins and ribosomes in all cellular organisms; conserved codon decoding and translation machinery
• Homology — relationship by common ancestry; "90 % homology" is imprecise because identity is the measurable quantity
• Orthologs and paralogs — separated by speciation versus gene duplication
• Alignment — matches corresponding positions; raw mismatch counts ignore repeated substitutions, indels and rate variation
• Example — in four hypothetical 12-base sequences, A–B differ at 1 position, A–C at 3, A–D at 6
• Limits — this alone cannot establish a species tree; more sequences and an explicit model are required
• Conserved domains — active sites, ATP-binding motifs and folding cores suggest function, but activity assays and genetic tests are still required

Knowing the sequence is not knowing the function; expression data suggest candidates, perturbation tests establish causation.

• Genomics vs functional genomics — the first catalogues DNA, the second tests how that information is used
• Methods — RNA-seq for transcript abundance, proteomics for protein amount and modification, gene perturbation for causality
• Expression ≠ activity — translation rate, degradation, post-translational modification, localisation and substrate supply all intervene
• Correlation ≠ causation — controls, biological replicates and independent validation are required
• Perturbation — knock out the candidate gene, compare phenotypes, then rescue by reintroducing the gene

A variant is not a cause; pathogenicity needs several independent lines of evidence.

• Cross-species comparison — identifies conserved genes, lineage-specific duplications and losses, and regulatory regions
• Model organisms — orthologs suggest initial hypotheses about human gene function
• Most variants are benign — pathogenicity requires population frequency, segregation in families, functional assays, clinical phenotype and replication
• Conserved residue changes — a clue to functional importance, not proof of disease causation
• Applications — antimicrobial resistance tracking, tumour genome analysis, rare disease variant interpretation
• Interpretation — sequence, expression, protein function, environment and clinical data must be read together

Data tables for this section, shown on click and printed in the appendix.