Evolutionary Biology

How old is Earth and what were early conditions like?

Around 4 billion years old. Early conditions were drastically different, extremely hot, very different atmospheric composition, no free oxygen and no life. Life arose at a specific point from non-living chemistry.

What is LUCA and why is it significant?

LUCA - Last Universal Common Ancestor, the single ancestral organism from which all life on Earth descended. It explains why fundamental biology is conserved across all domains: shared biochemistry, cellular organisation and genetic code.

What does the common ancestry of all life explain?

Why all living organisms share common features because they descended from LUCA:

• Dependence on water

• Shared chemical building blocks (carbs, lipids, amino acids, nucleic acids)

• Cellular organisation, enclosed by a plasma membrane

• Metabolism, extraction and conversion of energy

• Dna-based inheritance

What is metabolism?

Extraction and conversion of energy from the environment within a cell, includes uptake, conversion of molecules and excretion of by-products. It is a defining feature of life.

What is a nucleotide and what are its components?

Basic building blocks of DNA and RNA. Each nucleotide consists of a pentose sugar (deoxyribose in DNA and Ribose in RNA), a phosphate group and a nitrogenous base. Nucleotides are linked in a chain by phosphate bonds to form a polynucleotide strand whose sequence of bases encodes genetic information.

What is the difference between DNA and RNA?

DNA uses thymine and serves as long term hereditary storage, the archive of evolution. RNA is single stranded, uses uracil instead of thymine and translates the genetic code to control protein production.

What is a gene and a genome?

A gene is a DNA sequence encoding a functional product. A genome is the entire set of DNA in an organism.

What is the central dogma of molecular biology?

DNA is replicated → transcribed to RNA → translated into protein. This describes the flow of genetic information in cells.

What is transcription?

Process by which a segment of DNA is used as a template to produce a complementary RNA molecule. It is the first step of gene expression.

What is translation?

Process by which an RNA molecule is read by a ribosome to produce a specific sequence of amino acids (a protein). It is the second step of gene expression.

What is an amino acid and a protein?

Amino acids are the monomers of proteins. There are 20 standard ones, each with a different side chain that determines its chemical properties. A protein is a chain of amino acids (polypeptide) that folds into a 3D shape to carry out a specific function. Proteins are the primary molecular machines of the cell.

What is gene expression?

The process of transcription (DNA→RNA) plus translation (RNA→Protein), resulting in a functional gene product.

What is the RNA world hypothesis?

The proposal that RNA preceded both DNA and proteins. RNA can both store information and catalyse reactions (ribozymes), making it a plausible first self replicating molecule.

What is a ribozyme and why is it significant?

An RNA molecule that acts as a biological catalyst. Ribozymes show that early life may not have required proteins for catalysis, supporting the RNA world hypothesis.

What sequence of events does the RNA world hypothesis propose?

1. Self replicating RNA molecules arise

2. RNA supports formation of catalytic proteins

3. Proteins improve replication and metabolism efficiency

4. DNA evolves as a more stable information store

What did the Miller-Urey prebiotic synthesis experiments in the 1950s demonstrate?

Simulated early Earth atmosphere with simulated lightning. Result: spontaneous formation of amino acids and other organic molecules, the chemical building blocks of life can arise abiotically, without life already existing.

What were ‘cold chemistry’ experiments and what did they show?

Stanley Miller sealed atmospheric components and cooled them for 27 years. Amino acids and nucleotide bases were still produced, demonstrating that time and temperature variation does not prevent organic molecule formation. Building blocks of life arise without life processes.

How might organic molecules have arrived on early Earth from space?

Via comets and meteorites. The Murchison meteorite from Australia in 1969 contained amino acids and organic molecules unique to life, key evidence for delivery from space. Martian meteorites also contain traces of water and organic molecules.

What is the ‘primordial soup’ concept?

Hypothesis that small organic molecules accumulated and concentrated in early Earth environments, where catalysts enabled polymerisation into larger molecules. Key proposed environments: silicates in clay (mineral surfaces scaffold monomer assembly), metals in hydrothermal vents (anaerobic, metal-ion catalysis) and hot pools (heat concentrates monomers).

What are protocells?

Simple lipid spheres considered precursors to true cells. They lack a nucleus or internal structures but can separate an internal environment from the outside.

What are prokaryotes?

True cells without a nucleus or internal membrane bound organelles. They were the first true cells, appearing approximately 3.5 billion years ago. Include two domains: Bacteria and Archaea. Fossil evidence found in ancient rocks from this period.

What is an organelle?

Membrane-bound structure within a eukaryotic cell that performs a specialised function. Organelles are absent in prokaryotes.

What is endosymbiosis theory?

Larger host cell engulfed smaller prokaryotic cells but did not digest them, the engulfed cells became permanently integrated as organelles, with genes gradually transferring to the host nucleus. Mitochondria originated from aerobic bacteria (alpha-proteobacteria); chloroplasts from cyanobacteria. Both retain their own DNA and ribosomes.

What is the endomembrane system and how did the nucleus arise?

The nucleus and endoplasmic reticulum likely arose by infolding and fusion of the plasma membrane of an ancestral prokaryote. This endomembrane system forms the internal membrane network of eukaryotic cells.

What role did cyanobacteria play in Earth’s early evolution?

They performed photosynthesis using light, CO₂ and water, producing oxygen as a by-product. This accumulated in the atmosphere, fundamentally changing Earth’s chemistry and enabling the diversification of aerobic life.

What is the Great Oxidation Event?

The gradual accumulation of free oxygen in Earth’s atmosphere caused by cyanobacterial photosynthesis, ~2.4 BYA. Before cyanobacteria, Earth’s atmosphere contained virtually no free oxygen. Increased O₂ enabled aerobic metabolism and drove rapid diversification of new life forms.

What is the real pattern of biodiversity through deep time?

Decimation and diversification, not a smooth cone of increasing diversity. Some lineages diversify, others go extinct. Many Cambrian body plans have no modern equivalents. The Cambrian explosion, ~500 MYA, produced higher diversity of body plans than today, preserved in the Burgess Shale.

What is the Cambrian explosion?

Rapid diversification of animal body plans ~500 MYA, preserved in the Burgess Shale. Higher diversity of body plans in the Cambrian than today, but lower species diversity. Demonstrates the real pattern: decimation and diversification, not smooth progressive increase.

What is convergent evolution and an example?

Independent evolution of similar traits in unrelated lineages driven by similar selection pressures.

Example: Birds and bats evolved wings independently

What is a lineage?

Sequence of ancestral and descendant populations, species or individuals connected by an unbroken line of descent through time.

What is biodiversity through deep time shaped by?

Diversification (branching of new lineages) and extinction (loss of lineages). Evolution does not produce a smooth, ever-increasing diversity - extinctions are as much a part of the story as speciation.

How does the Earth’s atmosphere provide evidence for life and what did Lovelock propose?

Earth’s atmosphere is far from thermodynamic equilibrium, it contains ~21% O₂ and unsaturated water vapour, maintained by living organisms. In 1965, James Lovelock proposed detecting life on other planets by looking for atmospheric disequilibrium. This forms the basis of the Gaia hypothesis, Earth is a self-regulating system.

What did the viking programme find and what did later Mars missions show?

Viking (1975-76): one experiment appeared to show metabolism but two others failed to detect organic molecules, later interpreted as non-biological chemistry from highly oxidising soil conditions (perchlorates). Key lesson: chemistry can mimic biological signals. Curiosity rover later found organic matter in 3 billion year old mudstones at Gale Crater, evidence of past rather than current life.

What is the null hypothesis and can it be proven true?

A default assumption of no effect or pattern. It cannot be proven true - it can only be rejected or failed to be rejected based on evidence. (e.g. ‘all swans are white’ was disproven by one black swan).

What are the four things life can be defined by for detection purposes?

Metabolism, reproduction, cellular organisation and genetic information.

What is the Titan life detection example?

Titan has liquid methane oceans, any life would be methane-based. The Cassini-Huygens probe in 2005 detected a drop in H₂ levels near the surface, initially exciting but ultimately inconclusive as non-biological explanations could not be excluded the Dragonfly mission by NASA is planned to reach Titan in 2034 for further investigation.

What is the K2-18b exoplanet example of potential life detection?

K2-18b is an exoplanet ~700 trillion miles away. The James Webb Space Telescope detected possible dimethyl sulphide (DMS) or dimethyl disulphide (DMDS) in its atmosphere. On Earth, these are produced exclusively by ocean plankton and microorganisms. Evidence is preliminary - ~3 in 1000 chance of being a statistical fluke; further observations are needed.

What does ‘absence of fossils is not proof of absence of life’ mean scientifically?

The fossil record is incomplete as organisms may not fossilise or fossils may not yet be found. Absence of evidence is not evidence of absence; this is a core principle of scientific reasoning applied to paleontology and life detection.

How might life detection work on other planets beyond mars?

On titan (methane-based environment), life could differ fundamentally from Earth life. On exoplanets, atmospheric chemistry can be analysed for signatures inconsistent with abiotic processes - e.g. oxygen and methane coexisting - as indirect evidence of potential biological activity. All such evidence remains indirect and uncertain.

What are the two main lines of evidence for evolution?

Fossil record (species appearing, changing and disappearing) and morphological similarities which include homologous structures from common ancestry and convergent evolution showing independent similar structures.

What is the fossil record and what does it show?

A historical record of biodiversity preserved in sedimentary rock layers (strata - deeper layers are older). Shows: the sequence organisms appeared (more complex forms in younger layers), extinction of lineages and new organisms appearing at particular points in time.

What is homology and how does it differ from convergent similarity?

Homology: traits shared by different species reflecting common ancestry, the same underlying structure modified for different functions (e.g. bat wing, human arm, whale flipper share the same bone arrangement). Convergent evolution: similar traits evolved independently in unrelated lineages due to similar selection pressures, producing analogous structures. Similarity alone does not distinguish them.

What is a taxon and what does monophyletic mean?

A taxon is any named group of organisms at any level of classification (species, genus, family, etc.). Monophyletic (clade) means a group comprising of a common ancestor and all of its descendants, the basis of modern phylogenetic classification.

What is phylogeny and what does phylogenetics study?

Phylogeny is a branching tree diagram representing relationships among taxa based on shared ancestry. Phylogenetics is the field that infers and interprets these relationships from morphological or molecular data.

What were Darwin’s key observations and three propositions?

Observations: complex fossils in younger rock layers, galapagos finches resemble mainland species but are distinct, offspring resemble but are not identical to parents and overproduction of offspring. Three propositions:

1. Species change over time

2. Divergent species share a common ancestor

3. Natural selection explains the changes.

What is endemism?

The phenomenon of a species being native to and restricted to a particular geographic area. Darwin observed that island species resembled nearby mainland species but were distinct, suggesting local divergence from a common ancestor.

What are the four requirements for natural selection to occur?

Overproduction of offspring which creates competition for resources, variation among individuals, heritability of traits and differential survival and reproduction.

What is evolution and how is it measured?

Genetic change within populations over time. It occurs at the population level, not individuals. Often measured as changes in allele frequencies across generations.

What is an allele?

One of two or more alternative versions of DNA sequence at a given locus in the genome.

What is a locus?

Specific, fixed position on a chromosome where a particular gene or genetic marker is located.

What is a chromosome?

Long, organised structure of DNA and associated proteins (hostones) that carries genes. Humans have 46 chromosomes (23 pairs). Chromosomes are the physical units that segregate during cell division (meiosis and mitosis), determining how alleles are transmitted from parent to offspring.

What is a genotype?

Specific combination of alleles an organism carries at one or more loci.

What is a phenotype?

Observable characteristics of an organism (physical, physiological or behavioural) resulting from its genotype interacting with its environment.

What is the difference between a homozygote and heterozygote?

Homozygote carries two identical alleles at a locus (AA or aa). A heterozygote carries two different alleles (Aa). In a diploid organism, both copies are expressed unless one is dominant and masks the other.

What is a population in biology?

Group of individuals of the same species living in the same area at the same time, among them mating and gene flow occur. The population is the fundamental unit of evolution - selection, drift and other evolutionary forces act.

What is a species?

Group of organisms that share common ancestry and reproductively isolated from other groups. i.e. they can interbreed and produce fertile offspring among themselves but not (rarely) with members of other species.

What is natural selection?

Process by which heritable traits that increase survival or reproductive success (fitness) become more common in a population over generations, while traits that reduce fitness become rarer. It requires variation, heritability and differential reproductive success and is the primary mechanism of adaptive evolution.

What is an example of contemporary evolution?

Industrial melanism in moths: environmental darkening increased predation on light morphs. Dark morphs had a higher survival rate, so the frequency of dark colouration increased over time. A genetic basis is essential for this to count as evolution.

What are the six mechanisms of evolutionary change?

Natural selection, mutation, gene flow, genetic drift, non-random mating and sexual selection.

What is a mutation?

Change in DNA sequence occurring during replication. Mutations are random (not directed towards need) and can be beneficial, neutral or deleterious.

What is a neutral mutation?

Mutation with no effect on the carrier’s fitness. Vast majority of all molecular changes are neutral. Neutral mutations accumulate by genetic drift at a rate equal to the mutation rate (K = μ), forming the basis of the molecular clock.

What is gene flow?

Movement of alleles between populations via migration or dispersal. It introduces or removes alleles and can homogenise or introduce new variation.

What is genetic drift?

Random, stochastic changes in allele frequencies arising from finite gamete sampling, no fitness differences required. Two mechanisms:

• Mendelian segregation: chance deviation from 50:50 in heterozygotes;

• Random mortality: chance deaths unrelated to fitness.

Effects are strongest in small populations and can cause fixation or loss of alleles by chance alone.

What is fixation?

When an allele reaches frequency 1.0, every individual in the population carries it and all alternative alleles are lost.

What is genetic variation and why is it essential for evolution?

Differences in DNA sequence among individuals within a population, arising from mutation, recombination and gene flow. Genetic variation is the raw material for evolution - without it, natural selection and genetic drift have nothing to act on and populations cannot adapt. Measuring genetic variation is a core goal of population genetics.

What is sexual selection?

Selection arising from differences in mating success. Can favour costly traits that improve reproductive access.

• Intrasexual: competition within a sex;

• Intersexual: mate choices between sexes.

A subset of natural selection acting specifically on reproductive success.

What is directional selection?

Selection that consistently favours one extreme of a trait distribution, shifting the population mean over time (e.g. darker moths becoming more common after industrial pollution).

What is stabilising selection?

Selection that favours intermediate phenotypes and acts against both extremes, reducing trait variance (e.g. birth weight in humans, very low or very high weights have higher mortality).

What is disruptive selection?

Selection that favours both extremes and acts against intermediate phenotypes, potentially generating polymorphism or driving population divergence.

What is niche construction?

When organisms modify their own environment through their activities and those modifications feed back to alter the selection pressures on themselves and other species (e.g. earthworms altering soil structure, beaver dams reshaping aquatic habitats).

How does development link genes to phenotype?

Development (physiology, cellular processes, environmental influences) is the process through which a genotype is converted into a phenotype. Because the same genotype can produce different phenotypes depending on environmental context, genetic effects are filtered before selection can act on them.

What are the two key frameworks for understanding evolution and how do they differ?

Traditional models emphasise genes and external environment. Developmental perspectives additionally emphasise phenotype construction and internal processes, recognising that selection acts on phenotypes shaped by development, not genes directly.

What is the Baldwin effect?

The idea that a plastic phenotypic response can precede and facilitate genetic evolution. If a plastic response improves fitness, selection favours genotypes that produce that response and the trait can eventually become genetically fixed through canalisation.

What does the Earth as an evolving system mean?

Life and Earth’s atmosphere have co-evolved. Life influences atmospheric chemistry and atmospheric chemistry influences life. Earth’s atmosphere is far from thermodynamic equilibrium precisely because of biological activity.

What is an adaptation and a spandrel?

An adaptation is a heritable trait favoured by selection because it increase reproductive success. A spandrel is a trait that appears functional but arose as a by product of selection on something else, apparent function does not prove adaptive origin. High fecundity can generate non-adaptive physiological side effects.

What is the difference between primary and secondary sexual traits?

Primary sexual traits are directly involved in reproduction (e.g. genitalia). Secondary traits influence mating success but are not required for gamete production (e.g. antlers, bright plumage). Secondary traits often impose survival costs yet persist because mating benefits outweigh viability costs.

What is a gamete and why does gamete size matter for sexual selection?

A gamete is a haploid reproductive cell produced by meiosis. Two gametes fuse at fertilisation to form a diploid zygote. The asymmetry in gamete size (anisogamy), large costly eggs vs many small sperm, is the starting point for understanding sex differences in sexual selection.

What is meiosis?

Specialised cell division that produces gametes. It halves chromosome number (2n→n) and includes recombination, the shuffling of genetic material between homologous chromosomes. Meiosis is the source of genetic variation transmitted to offspring and why offspring are not identical to parents.

What is anisogamy and why is it the starting point for sexual selection theory?

The difference in gamete size between sexes, few large, energetically costly eggs vs many small, cheap sperm. This asymmetry makes eggs the limiting reproductive resource and is the fundamental origin of sex differences in selection.

What is parental investment and why does it matter for sex roles?

Any investment in an offspring that increases that offspring’s fitness at a cost to the parent’s future reproductive success (e.g. incubation, nursing, provisioning). The sex that invests more becomes the limiting resource, intensifying selection on the other sex.

What is fecundity?

Reproductive capacity of an organism, number of offspring produced per unit time or per reproductive event. Distinct from fertility (ability to reproduce at all). Fecundity differences underlie much of life history theory.

What is the casual chain from anisogamy to sexual selection?

Anisogamy → parental investment asymmetry → biased operational sex ratio (OSR) → increased variance in reproductive success → potential for sexual selection.

What is the operational sex ratio (OSR)?

Ratio of sexually receptive males to receptive females at any given time. Often differs from the adult sex ratio due to differences in parental investment and recovery time between matings. Male-biased OSR increases competition among males.

What is Bateman’s gradient?

Slope of reproductive success against number of mates. Steeper slope indicates stronger sexual selection. Typically steeper in males, it predicts which sex experiences stronger selection but does not specify which traits will evolve.

What is an example of a role-reversed species and what does it demonstrate?

Phalaropes, females are more ornamented and compete for mates, males provide care. Females show a steeper Bateman’s gradient. Demonstrates that anisogamy-derived sex roles are not fixed, they shift depending on who invests most in offspring.

What is intrasexual selection and an example?

Competition within one sex for access to mates. Example: red deer stags, fighting success predicts harem size and directional selection favours larger antler size.

What is intersexual selection?

Mate choice between sexes, typically females choosing among males. Drives and maintains elaborate male ornaments through female preferences.

What are alternative reproductive tactics (ARTs)?

Strategies used by individuals that cannot compete via the dominant male strategy. Example: Sneaker males that fertilise eggs covertly without fighting, females-mimic males that bypass dominant male guarding. ARTs are maintained when fitness payoffs are frequency-dependent.

What is frequency-dependent selection?

When the fitness of a phenotype depends on how common it is in the population. Negative frequency-dependent (rare advantage) is a common mechanism maintaining polymorphisms such as alternative reproductive tactics (ARTs).

What is a polymorphism in biology?

Stable existence of two or more distinct phenotypes or genotypes within a population at frequencies too high to be explained by mutation alone. Polymorphisms can be maintained by balancing selection (e.g. heterozygote advantage, frequency-dependence) or reflect neutral variation. Examples: coat colour variance, blood groups, alternative mating strategies.

What does the guppy example illustrate about sexual selection tradeoffs?

Bright colouration increases female attraction but also increases predation risk (visibility cost). If predators are removed, viability costs fall and sexual selection may drive further ornament exaggeration, but outcome depends on strength of female preference and available genetic variation.

What is variance in reproductive success and why does it matter for sexual selection?

Difference among individuals in number of offspring produced. Sexual selection requires high, non-random variance linked to heritable traits. Without heritable variance, selection cannot change trait frequencies.

What is the tradeoff at the heart of sexual selection?

Exaggerated traits often reduce survival (viability cost). Sexual selection can favour traits away from the survival optimum because mating benefits outweigh viability costs.

What is a tradeoff?

When investment in one function reduces investment in another. Tradeoffs arise from limited energy and resources and are central to the evolution of life histories and sexually selected traits.

What is the direct benefits hypothesis of mate choice?

Females gain immediate reproductive benefits from choosing certain males - food, protection, resources or nuptial gifts. Does require assumptions about genetic quality.

How do nuptial gifts illustrate direct benefits?

Larger gifts increase mating duration and sperm transfer, directly increasing female fecundity or survival. The male’s value is in his resource provision, not his genes.

What is the indirect benefits/good genes hypothesis?

Female preference targets heritable genetic quality. Traits must be condition-dependent and costly to express. Offspring inherit improved viability or resistance from a high-quality father.

What is a condition-dependent trait?

Trait whose expression depends on the individual’s overall health and resource acquisition, only high-condition individuals can fully express it, making it an honest signal of underlying quality.

What is the handicap principle?

Costly traits act as honest signals of quality because only genuinely high quality individuals can survive despite the handicap. The cost is what makes the signal reliable, cheap signals can be faked.

What is Fisherian runaway selection?

Genetic correlation forms between male trait and female preference. Positive feedback amplifies both the trait and the preference across generations. Rapid trait exaggeration occurs until viability costs halt further change.