Evolution

Antibiotic resistance in bacteria — evolution by natural selection: Background: • Bacterial populations contain natural genetic variation (mutations occur at ~1 in 10⁶–10⁸ base pairs per generation) • Before antibiotic use, a few bacteria in a population may carry a random mutation that confers resistance (e.g., mutation in target protein of antibiotic, enzyme to degrade antibiotic) Step-by-step process: 1. Initial population: A large population of bacteria, mostly susceptible to antibiotic; rare resistant mutants present naturally 2. Antibiotic application (selective pressure): • Antibiotic kills susceptible bacteria • Resistant bacteria survive and reproduce 3. Survival of the fittest: • Resistant bacteria have a survival advantage in the presence of antibiotic • They rapidly multiply (bacteria divide every 20 minutes) 4. Selection: • Over generations, the proportion of resistant bacteria increases • Susceptible bacteria are eliminated; population becomes predominantly resistant 5. Result: • New population is predominantly antibiotic-resistant • This is Darwinian natural selection in action — variation + selective pressure + differential reproduction Key point: The antibiotic does NOT cause the mutation — resistance mutations existed before antibiotic exposure. The antibiotic selects for pre-existing resistant variants. Importance: • Explains why antibiotics must be taken for full course • Basis for the global problem of antibiotic-resistant 'superbugs' (MRSA, XDR-TB) • Classic example showing evolution is an observable, ongoing process

El Niño effects on Galapagos evolution: El Niño is a climate phenomenon involving warm Pacific Ocean currents that periodically affect the Galapagos Islands. Effects on Darwin's Finches (Peter and Rosemary Grant's observations): 1. El Niño years (warm, wet): • Heavy rainfall on Galapagos (1982–83 El Niño) • Small, soft seeds become abundant • Small-beaked finches (Geospiza fortis — medium ground finch) can eat soft seeds easily • Small-beaked birds have a survival advantage • Natural selection favours SMALLER beak size • After El Niño: average beak size in population decreases 2. La Niña / drought years (opposite of El Niño): • Dry conditions → small seeds become scarce • Only large, hard seeds remain • Large-beaked birds survive better • Natural selection favours LARGER beak size • After drought: average beak size increases Evolutionary significance: • The Grants observed measurable evolution (changes in beak size) within a single generation • El Niño provides a natural selection experiment • Demonstrates that environmental fluctuations drive directional and oscillating selection • Shows that evolution is not unidirectional — it can reverse with changing conditions Broader impact on Galapagos ecosystem: • El Niño events affect iguana populations, sea lion prey availability, and plant communities • Marine iguanas shrink in body length during El Niño food scarcity — a rapid adaptive response Conclusion: El Niño serves as a natural experiment demonstrating how environmental change directly drives natural selection and measurable evolutionary change.

The Human Genome Project (HGP) is considered a milestone because: 1. First complete map of human genetic blueprint: • Sequenced ~3 billion base pairs of the human genome • Identified approximately 20,000–25,000 protein-coding genes • Provided a complete reference human genome sequence 2. Medical and clinical applications: • Identification of disease-causing genes (e.g., BRCA1/2 for breast cancer, CFTR for cystic fibrosis) • Development of predictive genetic testing • Personalised medicine — tailoring treatment to individual's genome • Understanding multifactorial diseases (heart disease, diabetes, cancer) 3. Development of new technologies: • Drove development of high-throughput DNA sequencing • Led to bioinformatics as a discipline • Reduced cost of sequencing from billions to hundreds of dollars 4. Comparative genomics: • Revealed humans share 99.9% DNA with each other • 98–99% similarity with chimpanzee genome • Shed light on evolutionary relationships 5. Understanding genome organisation: • Revealed that only ~1.5% of human DNA codes for proteins • Large amounts of non-coding DNA (including regulatory elements, pseudogenes, repetitive sequences) • Led to ENCODE project (functional elements in genome) 6. Pharmacogenomics: • Understanding how genetic variation affects drug response • Allows dosage optimisation, avoids adverse drug reactions 7. Forensic applications: • DNA fingerprinting techniques improved • Identification of individuals in criminal cases The project was completed in 2003, and represents an extraordinary international scientific achievement involving researchers from 18 countries.

Punctuated Equilibrium (Gould and Eldredge, 1972): Traditional view (phyletic gradualism): • Darwin proposed gradual, slow, continuous evolution over long periods • Fossil record should show gradual transitions between species Problem with gradualism: • Fossil record shows SUDDEN appearance of new species and long periods of no change (stasis) • Missing transitional fossils puzzled evolutionary biologists Punctuated Equilibrium model: • Evolution occurs in BURSTS of rapid change (punctuations) separated by long periods of stability (equilibrium/stasis) Key features: 1. Stasis (equilibrium): • Species remain morphologically unchanged for millions of years (stasis) • Existing species are well-adapted to stable environments 2. Punctuations (rapid change): • Short geological periods of rapid change • New species appear suddenly in the fossil record • Often associated with geographic isolation of small populations 3. Allopatric speciation: • Small peripheral populations isolated from main population • Rapid genetic changes in small isolated populations (genetic drift, intense selection) • New species can evolve in ~10,000–100,000 years (rapid in geological terms) 4. Evidence: • Fossil record of horses, molluscs, trilobites • Cambrian explosion (~540 mya): most animal phyla appeared within ~10 million years Contrast with gradualism: • Gradualism: continuous, slow, smooth • Punctuated equilibrium: long stasis interrupted by rapid bursts Conclusion: The apparent gaps in the fossil record are not due to imperfection but reflect the actual pattern of evolution — long stability punctuated by rapid evolutionary change.

Hardy-Weinberg Principle (1908): In a large, randomly mating population, the allele and genotype frequencies remain constant from generation to generation UNLESS some agent acts to change them. Mathematical expression: For a gene with two alleles A (frequency p) and a (frequency q): • p + q = 1 • Genotype frequencies: p² (AA) + 2pq (Aa) + q² (aa) = 1 This is the Hardy-Weinberg equilibrium. Conditions for Hardy-Weinberg equilibrium to hold (population must satisfy ALL): 1. Large population size: • Random genetic drift (chance changes in allele frequency) are negligible in large populations • In small populations, drift can alter allele frequencies randomly 2. Random mating (panmixia): • All genotypes must mate with equal probability • No sexual selection or assortative mating 3. No mutations: • No new alleles being introduced or existing alleles being changed 4. No gene flow (no migration): • No alleles entering (immigration) or leaving (emigration) the population 5. No natural selection: • All genotypes have equal survival and reproductive success (equal fitness) • No allele is advantageous over another Agents that disturb H-W equilibrium (forces of evolution): • Mutation: creates new alleles • Natural selection: differential survival/reproduction • Genetic drift: random changes in small populations • Gene flow (migration): alleles moving between populations • Non-random mating: assortative mating, inbreeding Significance: Hardy-Weinberg equilibrium serves as a null hypothesis for evolution — any deviation indicates that evolutionary forces are acting.

Types of Natural Selection: 1. Directional Selection: • Favours one extreme phenotype; shifts the population mean in one direction • One end of the phenotypic distribution has highest fitness • Result: Population mean shifts toward favoured extreme over time • Examples: – Antibiotic resistance: resistant bacteria are favoured – Dark peppered moths (Biston betularia) in industrial areas: dark form (melanic) increased from rare to 90%+ in polluted areas where tree bark darkened with soot (industrial melanism) – Horse evolution: gradual increase in body size and toe reduction from Eohippus to Equus 2. Stabilising Selection (normalising selection): • Favours intermediate (average) phenotypes; eliminates extremes • Reduces variation; most individuals cluster around the mean • Occurs in stable environments • Examples: – Human birth weight: very small and very large babies have higher mortality; intermediate weight (~3.2 kg) has highest survival – Shell thickness in snails: too thin (vulnerable to predators), too thick (heavy, costly) — intermediate favoured 3. Disruptive Selection (diversifying selection): • Favours BOTH extreme phenotypes over intermediate forms • Can lead to bimodal distribution or even speciation • Occurs when environment is heterogeneous • Examples: – Darwin's finches: large and small beaks both favoured; intermediate size disadvantaged (different food sources) – Oyster colour: dark and light oysters survive on different substrates; medium grey are conspicuous on both – Salmon: large dominant males and small sneaker males both reproduce; intermediate-sized males less successful Summary: • Directional: one extreme favoured → shift in mean • Stabilising: intermediate favoured → reduced variation • Disruptive: both extremes favoured → increased bimodality