Mutations & Gene Editing → Natural Selection · 13 readings covered · Built from your last Kognity assignments
Teacher's Review Questions
Click any question to reveal the answer. Use these as your primary checklist — make sure you can answer each one without the prompt before the assessment.
State two derived characteristics of mammals.
Any two of the following — pick the ones you can defend in one sentence:
Hair / fur made of keratin covering the body (for insulation and sensory function).
Mammary glands that secrete milk to nourish young.
Three middle-ear bones (malleus, incus, stapes) — evolved from reptilian jaw bones.
A neocortex region of the brain (complex cognition).
Heterodont dentition — teeth differentiated into incisors, canines, premolars and molars.
A muscular diaphragm separating thoracic and abdominal cavities (for efficient breathing).
Endothermy with a four-chambered heart (note: birds also have these — they evolved independently, so on their own they're not unique to mammals).
Best two for an exam: hair/fur + mammary glands — these are uniquely mammalian (synapomorphies) and not found in any other class.
If two species share the same genus name, are they closely related?
Yes. The genus is the second-narrowest taxonomic rank (only the species rank is narrower), so two species in the same genus share a recent common ancestor and many derived characteristics. They belong to the same clade at that level and are usually morphologically and genetically very similar.
Examples: Panthera leo (lion) and Panthera tigris (tiger) share the Panthera genus — both are big cats and can even produce hybrids (ligers, tigons). Homo sapiens and the extinct Homo neanderthalensis shared the Homo genus and a common ancestor only ~600,000 years ago.
Caveat: "closely related" is relative. Two species in the same genus are more closely related to each other than to a species in a different genus — but less closely related than two populations of the same species.
List two causes of genetic mutations.
Mutations have two broad sources:
1. Spontaneous (endogenous) causes — DNA replication errors (the polymerase pairs the wrong base); chemical instability of DNA (depurination, deamination of cytosine to uracil); errors in DNA repair.
2. Induced causes (mutagens) — agents from the environment that damage DNA or increase the error rate:
Chemical mutagens — benzene, mustard gas, nitrous acid, tobacco tar.
Some viruses (e.g. HPV) — insert their DNA and disrupt host genes.
Best answer for "list two": (1) errors during DNA replication, and (2) exposure to mutagens such as UV light or ionising radiation.
What evidence is used to place species in a specific clade?
A clade is built using shared derived characters (synapomorphies) — features inherited from a common ancestor and not found in lineages outside the clade. The main evidence types are:
Molecular evidence (most reliable today) — DNA sequences, RNA sequences, and amino acid sequences of conserved proteins (e.g. cytochrome c, ribosomal RNA). The fewer the differences, the more recently the species shared an ancestor.
Morphological / anatomical evidence — homologous structures (e.g. the pentadactyl limb), bone structure, internal anatomy. Beware analogous structures from convergent evolution!
Embryological evidence — shared developmental stages (e.g. all vertebrate embryos have pharyngeal arches and a tail).
Fossil evidence — transitional fossils show ancestral features (e.g. Tiktaalik linking fish to tetrapods).
Behavioural and biochemical evidence — shared metabolic pathways, courtship rituals, etc.
In modern cladistics, molecular data (especially DNA) is now the primary evidence because it is quantitative, abundant, and less subject to convergent evolution than morphology.
List two causes of variation within a gene pool.
A gene pool is the total collection of all alleles in a population. Variation within it comes from:
1. Mutation — the original source of all new alleles. Without mutation there would be no variation.
2. Sexual reproduction / meiosis — shuffles existing alleles into new combinations via:
Crossing over in prophase I (recombines linked alleles);
Independent assortment in metaphase I (random orientation of bivalents);
Random fertilisation (any sperm × any egg).
Other contributors: gene flow (migration) bringing new alleles in from other populations, and genetic drift changing allele frequencies randomly.
Best answer for "list two": (1) mutation (new alleles), and (2) meiosis and sexual reproduction (new allele combinations).
Explain how variation contributes to evolution by natural selection.
Natural selection requires variation. Without it, every individual would have identical fitness and there would be nothing for selection to act on. The logic flows in five steps:
(1) Within a population, individuals show heritable variation in their traits (caused by mutation and sexual reproduction).
(2) Populations overproduce offspring — more are born than the environment can support, creating competition.
(3) Some variants happen to be better suited to the environment (faster, better camouflaged, better at finding mates, more disease-resistant…).
(4) These individuals are more likely to survive and reproduce — they have higher fitness. They pass their alleles to the next generation in greater numbers.
(5) Over many generations, the frequency of beneficial alleles increases in the gene pool — the population becomes better adapted to its environment. This is evolution.
Concrete example: in the peppered moth, the population originally had both light (typica) and dark (carbonaria) forms — that was the variation. When industrial soot darkened tree bark, dark moths survived predation by birds more often. Over ~50 years the dark allele's frequency rose from <2% to >95% in industrial cities. Variation supplied the raw material; selection sorted it.
Key point: without variation, no evolution by natural selection is possible. Selection cannot create new traits — it can only act on the variation that already exists.
Outline the requirements for speciation to occur.
Speciation is the formation of a new species. For it to occur, four conditions must combine:
1. Genetic variation within the population — supplied by mutation and sexual reproduction. Without variation, divergence is impossible.
2. Some form of isolation that prevents gene flow between two parts of the population. This can be:
Geographic (allopatric) — a physical barrier such as a mountain range, river, ocean, or new ice age.
3. Different selection pressures acting on the two isolated populations — different climates, predators, food sources, etc. This drives divergence.
4. Time — enough generations for genetic differences to accumulate until the two populations can no longer interbreed to produce fertile offspring, even if reunited.
The bottom line: speciation = variation + isolation (no gene flow) + divergent selection + time → reproductive isolation between the two new species.
Describe the three domains of organisms.
Carl Woese (1990) proposed splitting all life into three domains based on ribosomal RNA sequence differences:
Bacteria — prokaryotic (no membrane-bound nucleus); single circular chromosome; cell walls made of peptidoglycan; reproduce by binary fission; very diverse metabolisms. Examples: E. coli, Streptococcus, cyanobacteria.
Archaea — also prokaryotic in cellular organisation, but biochemically distinct. Cell walls do not contain peptidoglycan; membrane lipids have ether-linked branched isoprene chains (Bacteria have ester-linked straight-chain lipids); their RNA polymerase and ribosomes are more like those of eukaryotes. Many live in extreme environments — hot springs, deep-sea vents, salt lakes — but they also live in normal soils, oceans, and your gut. Examples: methanogens, halophiles, thermophiles.
Eukarya — eukaryotic cells with a true membrane-bound nucleus and other membrane-bound organelles (mitochondria, ER, Golgi, chloroplasts in plants). Includes four traditional kingdoms: Protista (single-celled eukaryotes), Fungi, Plantae, and Animalia.
Evolutionary relationship: Archaea and Eukarya are more closely related to each other than either is to Bacteria — the eukaryotic cell is thought to have originated from an archaeal ancestor that engulfed a bacterium (which became the mitochondrion).
What is the difference between allele frequency and a gene pool?
A gene pool is the total collection of all alleles for every gene in a population — the entire "library" of genetic material available. It's a description of the population's genetic content.
An allele frequency is the proportion of one particular allele relative to all the alleles for that gene in the population. It's a number between 0 and 1 (or expressed as a percentage).
Analogy: if the gene pool is a bag of marbles where each marble is an allele, then the allele frequency is the percentage of marbles that are red (or blue, or green).
Worked example: in a population of 100 diploid pea plants, the gene for flower colour has two alleles — purple (P) and white (p). That's 200 total alleles. If 140 of them are P and 60 are p, then:
The gene pool contains the P and p alleles (and many other genes' alleles).
The allele frequency of P = 140/200 = 0.70 (70%).
The allele frequency of p = 60/200 = 0.30 (30%).
Key: evolution is defined as a change in allele frequencies in a gene pool over generations.
Compare allopatric and sympatric speciation.
Both produce new species, but they differ in the type of isolating mechanism.
Similarities:
Both require reproductive isolation that prevents gene flow.
Both rely on genetic variation and divergent selection (or drift) to drive populations apart.
Both produce two (or more) species from one ancestral species.
Galápagos finches; Grand Canyon squirrels (Abert's vs Kaibab); London Underground mosquito
Modern bread wheat (polyploidy); cichlid fish in Lake Victoria (mate preference); apple maggot fly
Summary sentence: Allopatric speciation requires a geographic barrier to split the population before reproductive isolation evolves, whereas sympatric speciation produces reproductive isolation within a single geographic area, usually via polyploidy, niche differentiation, or sexual selection.
D1.3 · SL + HL
1. Mutations & Gene Editing
Summary
A mutation is a permanent change in the DNA base sequence. Mutations arise either spontaneously (DNA replication errors, depurination, deamination) or are induced by mutagens (UV light, ionising radiation, chemicals like benzene). Mutations in somatic cells affect only the individual and can cause cancer; mutations in germline cells are passed to offspring and supply the raw genetic variation that fuels evolution.
Single-base substitutions can be silent (no amino-acid change, because of redundancy in the genetic code), missense (one amino acid swapped — e.g. sickle-cell anaemia: GAG→GTG, Glu→Val at codon 6 of β-globin), or nonsense (creates a premature stop codon, truncating the protein). Insertions/deletions of bases not in multiples of three cause a frameshift, scrambling all downstream codons.
HLGene editing with CRISPR-Cas9 uses a guide RNA to direct the Cas9 nuclease to a complementary DNA sequence, where it cuts both strands. The cell's repair machinery (NHEJ or HDR) then either disables the gene (knockout) or inserts a chosen sequence (knock-in). Applications include sickle-cell therapy, drought-resistant crops, gene drives in mosquitoes, and human germline editing — which raises serious ethical questions.
Key Terms
MutationA permanent change in the DNA nucleotide sequence.
MutagenAn agent that increases the mutation rate (e.g. UV, X-rays, benzene, mustard gas).
SubstitutionOne base is replaced by another (silent, missense, or nonsense).
Insertion / DeletionAddition or removal of one or more nucleotides; causes frameshift if not a multiple of 3.
Frameshift mutationShifts the reading frame downstream of the indel — usually catastrophic for the protein.
Silent mutationBase change that does not alter the amino acid (due to the degenerate code).
Missense mutationBase change that produces a different amino acid (e.g. HbS in sickle-cell).
Nonsense mutationBase change that produces a premature stop codon, truncating the protein.
Somatic vs germlineBody-cell vs gamete-line mutation; only germline mutations are heritable.
Chromosomal mutationDeletion, duplication, inversion, or translocation of a chromosome segment.
AneuploidyAn abnormal chromosome number (e.g. trisomy 21 → Down syndrome) from non-disjunction.
CRISPR-Cas9 HLA bacterial defence system repurposed for gene editing: a guide RNA targets Cas9 to a specific DNA sequence to make a precise double-stranded cut.
Gene knockout HLDeliberately disabling a gene to study its function or remove a harmful variant.
SNP HLSingle-nucleotide polymorphism — a one-base difference between individuals; useful as a genetic marker.
Exam tip: When asked to explain why sickle-cell is a "missense" mutation, be explicit: a single base substitution (A→T) in the β-globin gene changes one codon (GAG → GTG), causing one amino acid substitution (Glu → Val) at position 6, which makes haemoglobin polymerise under low O₂.
Practice Questions
Distinguish between a silent, missense, and nonsense mutation.
All three are point substitutions. Silent: the new codon still codes for the same amino acid (no protein change). Missense: the new codon codes for a different amino acid (protein altered, may or may not still function). Nonsense: the new codon is a stop codon, so translation halts early and the protein is truncated.
Why are frameshift mutations usually more harmful than substitutions?
A frameshift shifts the reading frame for every downstream codon, so every amino acid after the mutation is wrong and a premature stop codon is likely. A substitution affects only one codon.
Explain the role of non-disjunction in producing trisomy 21.
During meiosis I (or II), homologous chromosomes 21 fail to separate. One gamete ends up with two copies of chromosome 21; when this fertilises a normal gamete, the zygote has three copies (47, XX/XY +21) — Down syndrome.
HL Outline how CRISPR-Cas9 edits a specific gene.
A short guide RNA (gRNA) with a sequence complementary to the target gene is delivered into the cell along with the Cas9 endonuclease. The gRNA base-pairs with the target DNA; Cas9 makes a double-strand break. The cell repairs the break by either NHEJ (error-prone, knocks the gene out) or, if a donor template is supplied, HDR (knocks in a chosen sequence).
HL Give one benefit and one ethical concern of human germline editing.
Benefit: heritable correction of disease-causing alleles (e.g. eliminating Huntington's). Concern: off-target effects are heritable; "designer babies" and consent of future generations; widening inequality if only the wealthy access it.
D2.2 · HL only
2. Gene Expression HL
Summary
Every cell in a multicellular organism has the same genome, yet a neuron and a liver cell look and behave nothing alike — because they express different sets of genes. Gene expression is the controlled process by which information in a gene is converted into a functional product (usually a protein). It is regulated at many levels: transcription initiation, RNA processing, mRNA stability, translation, and post-translational modification.
Transcription factors are proteins that bind to promoter or enhancer sequences and either recruit or block RNA polymerase II. Some factors are activators, others are repressors. The same gene can be switched on in one cell type and off in another depending on which factors are present.
Epigenetic regulation changes gene expression without altering the DNA sequence itself. The two main mechanisms are DNA methylation (addition of –CH₃ groups to cytosine bases in CpG islands — usually silencing the gene) and histone modification (acetylation typically opens chromatin and increases expression; methylation can do either). These marks can be inherited through mitosis, and sometimes through meiosis — explaining how the Dutch Hunger Winter famine altered the health of grandchildren of women who were pregnant during the winter of 1944–45.
Key Terms
Gene expressionThe process by which a gene's information is used to synthesise a functional product (protein or RNA).
PromoterDNA sequence upstream of a gene where RNA polymerase and transcription factors bind.
Enhancer / SilencerRegulatory DNA sequences (can be far from the gene) that increase or decrease transcription.
Transcription factorProtein that binds DNA to activate or repress transcription of a target gene.
EpigeneticsHeritable changes in gene expression that do not involve changes to the DNA sequence.
DNA methylationAddition of a methyl group (–CH₃) to cytosine in CpG dinucleotides; usually silences the gene.
Histone acetylationAddition of acetyl groups to histone tails; loosens chromatin and increases transcription.
Chromatin (eu- vs hetero-)Euchromatin is loosely packed and actively transcribed; heterochromatin is condensed and silent.
Differential gene expressionDifferent genes being transcribed in different cell types — the basis of cell differentiation.
Environmental epigenetic effectExternal factor (diet, stress, toxin) that alters epigenetic marks — e.g. Dutch Hunger Winter cohort.
Exam tip: If asked "How can identical twins have different phenotypes?" — the answer is differential gene expression driven by epigenetic differences accumulated over their lifetimes (different diets, stress, exposures methylating different genes).
Practice Questions
Explain how transcription factors control gene expression.
Transcription factors bind to specific DNA sequences (promoters, enhancers, silencers) and either recruit RNA polymerase II and the rest of the pre-initiation complex (activators) or block its assembly/binding (repressors). The same gene can therefore be transcribed in one cell and silent in another depending on which transcription factors are present.
How does DNA methylation silence a gene?
Methyl groups added to cytosines in CpG islands within the promoter physically block transcription-factor binding and also recruit proteins (e.g. MeCP2) that condense the chromatin around the promoter into heterochromatin, preventing RNA polymerase II access.
Describe one piece of evidence that the environment can affect gene expression across generations.
The Dutch Hunger Winter cohort: babies whose mothers were starved during early pregnancy had altered DNA methylation patterns at the IGF2 gene that persisted into adulthood and were correlated with higher rates of obesity, diabetes and cardiovascular disease — and some of these epigenetic patterns were detectable in their children.
How do histone modifications regulate transcription?
Histones have N-terminal tails that can be modified. Acetylation by HATs neutralises the positive charge on lysines, weakening histone–DNA binding so chromatin opens (active). Deacetylation by HDACs tightens chromatin (silent). Histone methylation can do either, depending on the residue.
D3.2 · SL + HL
3. Inheritance
Summary
Mendel's law of segregation states that the two alleles for each gene separate during gamete formation so each gamete carries one allele. A monohybrid cross between two heterozygotes (Aa × Aa) gives a 3:1 phenotypic ratio in the offspring. Mendel's law of independent assortment states that alleles of genes on different chromosomes segregate independently, giving the classic 9:3:3:1 ratio in a dihybrid cross (AaBb × AaBb).
Not all inheritance is so simple. In incomplete dominance (e.g. snapdragon flower colour) the heterozygote shows an intermediate phenotype. In codominance (e.g. ABO blood groups) both alleles are fully expressed (AB blood type has both A and B antigens). Multiple alleles means a single gene has >2 possible alleles in the population (IA, IB, i for ABO). Sex linkage (e.g. haemophilia, red-green colour blindness) is when a gene sits on the X chromosome — males (XY) need only one recessive allele to express the phenotype, females need two.
Pedigree analysis uses family trees to deduce inheritance patterns. Autosomal recessive traits skip generations; autosomal dominant traits appear in every generation; X-linked recessive traits affect mostly males and are inherited through carrier mothers.
HL The chi-squared test (χ²) is used to test whether observed offspring ratios deviate significantly from those expected. Linked genes sit on the same chromosome and do not assort independently — they tend to be inherited together unless separated by crossing over. The greater the distance between two linked genes, the higher the recombination frequency (used to build genetic maps).
Key Terms
AlleleOne of two or more alternative forms of a gene at a given locus.
Genotype / PhenotypeThe combination of alleles an organism carries / the observable trait it produces.
Homozygous / HeterozygousTwo identical alleles / two different alleles at a locus.
Dominant / RecessiveAn allele that is expressed in the heterozygote / only expressed when homozygous.
Incomplete dominanceHeterozygote shows a phenotype intermediate between the two homozygotes.
CodominanceBoth alleles in the heterozygote are fully expressed (e.g. ABO type AB).
Multiple allelesA gene with more than two allele variants in the population.
Sex linkageA gene on a sex chromosome (X or Y) — produces unequal inheritance between sexes.
CarrierA heterozygote for a recessive trait — phenotypically normal but able to transmit.
Test crossCross of an unknown genotype to a homozygous recessive to reveal the unknown genotype.
Punnett squareDiagram for predicting offspring genotype/phenotype ratios.
PedigreeDiagram showing inheritance of a trait through generations of a family.
Linked genes HLGenes located on the same chromosome — inherited together unless separated by crossing over.
Recombination frequency HLProportion of recombinant offspring; proxy for distance between linked genes.
Chi-squared test HLStatistical test of whether observed ratios fit expected ones. χ² = Σ(O−E)²/E.
Polygenic inheritance HLA phenotype controlled by many genes — produces continuous variation (e.g. height, skin colour).
Exam tip: For sex-linked questions, always write the genotypes with the gene on the X — e.g. XHXh for a carrier female, XhY for an affected male. Never forget to include the Y in male genotypes.
Practice Questions
State Mendel's two laws and which type of cross demonstrates each.
Law of segregation: the two alleles of a gene separate into different gametes during meiosis — shown by a monohybrid cross (3:1). Law of independent assortment: alleles of genes on different chromosomes are inherited independently — shown by a dihybrid cross (9:3:3:1).
A man with blood type AB marries a woman with blood type O. What are the possible blood types of their children?
Father: IAIB. Mother: ii. Children get one allele from each parent → either IAi (type A) or IBi (type B), in equal proportions. No child can be AB or O.
A colour-blind man (X-linked recessive) marries a non-carrier woman. Predict the phenotypes of their sons and daughters.
Father XbY × Mother XBXB. Daughters: all XBXb — carriers, normal vision. Sons: all XBY — normal vision, not carriers.
In a pedigree, what features suggest an autosomal recessive trait?
Trait skips generations; can appear in offspring of two unaffected parents (both must be carriers); affects males and females equally; often associated with consanguinity.
HL A dihybrid test cross gives 88 AB : 12 Ab : 13 aB : 87 ab offspring. What does this suggest?
The expected ratio under independent assortment is 1:1:1:1 (50:50:50:50). The huge over-representation of parental types (AB, ab) and under-representation of recombinants (Ab, aB) shows the genes are linked. Recombination frequency = (12+13)/200 = 12.5%, so the genes are about 12.5 map units apart.
HL When would you reject the null hypothesis in a chi-squared test of inheritance?
When the calculated χ² value exceeds the critical value at the chosen significance level (usually p = 0.05) for the appropriate degrees of freedom (df = number of phenotypic classes − 1). This means the observed ratio differs significantly from the expected — assumption (e.g. independent assortment) is rejected.
A3.1 · SL + HL
4. Diversity of Organisms
Summary
Life on Earth is astonishingly diverse — current estimates put species number between 8 and 30 million, of which only about 1.9 million have been formally described. The biological species concept defines a species as a group of organisms that can interbreed to produce fertile offspring. This works well for sexually-reproducing extant animals, but fails for asexual organisms, fossils, and organisms that hybridise (e.g. polar × grizzly bears).
Variation within a species arises from genetic differences (mutation, sexual reproduction shuffling alleles via meiosis and fertilisation) and from environmental influences on phenotype (e.g. hydrangea flower colour responds to soil pH). Variation can be discrete (categorical — e.g. blood type) or continuous (a spectrum — e.g. height, skin colour); continuous variation usually arises from polygenic inheritance plus environmental factors.
The binomial naming system (Linnaeus, 1758) gives every species a unique two-part Latin name: Genus species (e.g. Homo sapiens). The genus is capitalised, the species is lowercase, and the whole name is italicised (or underlined when written by hand). Above genus, organisms are grouped into family → order → class → phylum → kingdom → domain (the three domains being Bacteria, Archaea, Eukarya).
Key Terms
SpeciesA group of organisms that can interbreed and produce fertile offspring (biological species concept).
PopulationAll members of one species living in the same area at the same time.
VariationDifferences between individuals; can be discrete or continuous.
Genetic variationDifferences in DNA sequence between individuals — the raw material for natural selection.
Phenotypic variationDifferences in observable traits; influenced by genes + environment.
Discrete variationDistinct categories with no overlap (e.g. ABO blood group, attached/free earlobes).
Continuous variationA gradient of values (e.g. height, mass) — usually polygenic + environmental.
Binomial nomenclatureTwo-name Latin system: Genus species, italicised, genus capitalised.
Three-domain systemBacteria, Archaea, Eukarya — based on ribosomal RNA differences (Woese, 1990).
HybridOffspring of two different species (e.g. liger). Usually sterile.
Practice Questions
State two limitations of the biological species concept.
(1) It cannot be applied to asexually-reproducing organisms (e.g. bacteria) where there is no interbreeding to assess. (2) It cannot be tested on extinct species known only from fossils, nor on organisms separated by geography (allopatric populations) that have never had the chance to interbreed.
Distinguish between discrete and continuous variation, giving one example of each.
Discrete: distinct categories controlled by one or few genes; little/no environmental influence — e.g. ABO blood group. Continuous: a smooth range of values, controlled by many genes plus environment — e.g. human height.
Why is binomial nomenclature important?
It gives every species a unique, universal scientific name regardless of language, avoiding the confusion of multiple common names (e.g. "cougar/puma/mountain lion" all = Puma concolor). It also signals taxonomic relationships through shared genus names.
Explain how meiosis and fertilisation contribute to genetic variation.
Meiosis introduces variation in three ways: (1) crossing over in prophase I exchanges segments between homologous chromosomes; (2) independent assortment in metaphase I randomly orients each bivalent (223 combinations in humans); (3) random fertilisation combines genetically unique gametes. Together this produces effectively unlimited offspring genotypes.
A3.2 · SL + HL
5. Classification & Cladistics
Summary
Modern classification arranges organisms by evolutionary relationship rather than superficial similarity. A clade is a group consisting of a common ancestor and all of its descendants — a "monophyletic" group. Cladistics uses shared derived characters (synapomorphies) to build cladograms — branching diagrams that hypothesise evolutionary relationships. Branch points are nodes representing common ancestors.
Cladograms can be built from morphological features (bone shape, embryonic structures) but are now most reliably built from molecular evidence — typically comparing DNA, RNA or amino-acid sequences. The greater the number of differences between two species in a given gene, the longer ago they shared a common ancestor (assuming a roughly constant molecular clock).
Modern classification has reshuffled some traditional groups. The "reptile" group (Reptilia) is paraphyletic — it excludes birds, which are actually descended from theropod dinosaurs. To make a monophyletic clade, biologists group reptiles + birds together as Sauropsida. Fungi are now known to be more closely related to animals than to plants.
Key Terms
TaxonomyThe science of naming, describing and classifying organisms.
Hierarchy of taxaDomain → Kingdom → Phylum → Class → Order → Family → Genus → Species.
CladeA group containing a common ancestor and all of its descendants (monophyletic).
CladogramA branching diagram showing hypothesised evolutionary relationships based on shared derived characters.
NodeA branch point on a cladogram — represents a common ancestor.
SynapomorphyA shared derived character — evidence of common ancestry within a clade.
Homologous structuresStructures with a common evolutionary origin, possibly different functions (e.g. pentadactyl limb).
Analogous structuresStructures with similar function but different evolutionary origin (e.g. bird wing vs insect wing) — convergent evolution.
Molecular clockUse of accumulated DNA/protein differences to estimate the time since two species diverged.
Paraphyletic groupA group that includes a common ancestor but not all of its descendants (e.g. traditional "reptiles" — excludes birds).
Polyphyletic groupA group whose members do not share a recent common ancestor (e.g. "warm-blooded animals" — birds + mammals evolved endothermy independently).
Exam tip: When reading a cladogram, two species are most closely related if their lineages converge at the most recent node — not if they look most similar! Branch length does not always represent time.
Practice Questions
What is a clade, and why is "reptiles" not a true clade?
A clade is a monophyletic group containing a common ancestor and all its descendants. Traditional Reptilia is paraphyletic because birds descended from the same ancestor as crocodilians but are excluded from the group. To make a true clade you must either remove crocodilians or include birds (Sauropsida).
Explain how DNA sequence data can be used to construct a cladogram.
Sequence the same gene (often a conserved one like cytochrome b or 16S rRNA) from each species. Align the sequences and count nucleotide differences between every pair. Use an algorithm (parsimony, maximum likelihood) to build the tree topology that requires the fewest mutational steps. The more differences between two sequences, the longer ago they diverged.
Distinguish between homologous and analogous structures with examples.
Homologous: share an evolutionary origin but may differ in function — e.g. the pentadactyl limb is modified into a human arm, a bat wing, a whale flipper, a horse leg. Analogous: similar function but independent origins — e.g. the wings of a bird (modified forelimb) and an insect (cuticle outgrowth) — convergent evolution.
What is the molecular-clock hypothesis, and what assumption does it make?
Mutations accumulate in a given gene at a roughly constant rate over time, so the number of differences between two species' sequences is proportional to the time since they diverged. Assumes the mutation rate is approximately constant and that most mutations are neutral (not strongly selected).
D4.1 · SL + HL
6. Evolution & Speciation
Summary
Evolution is heritable change in the characteristics of populations over generations. Evidence comes from many independent lines: the fossil record (transitional fossils like Tiktaalik and Archaeopteryx); comparative anatomy (homologous structures, vestigial organs like the human appendix); biogeography (closely related species on adjacent islands — Galápagos finches); artificial selection (the diversity of dog breeds in a few thousand years); and most powerfully molecular biology (universal genetic code, shared genes between distant species, retroviral insertions).
Speciation is the formation of new species. It requires reproductive isolation — i.e. two populations stop exchanging genes. Allopatric speciation happens when populations are physically separated (mountain range, river, ocean) and diverge in different environments — the most common mechanism. Sympatric speciation happens without geographic separation, typically through behavioural, temporal, or polyploidy isolation.
HL Reproductive isolating mechanisms fall into prezygotic (no fertilisation: temporal, behavioural, mechanical, gametic) and postzygotic (fertilisation occurs but offspring are inviable or sterile, e.g. mule). Polyploidy (multiplication of chromosome sets) is a major instant speciation mechanism in plants — about 70% of angiosperm species have a polyploid ancestor (e.g. modern bread wheat is hexaploid).
Adaptive radiation is the rapid diversification of a lineage into many descendant species that exploit different niches. Classic examples: Darwin's finches on the Galápagos (13 species from one ancestor), cichlid fish in African Rift lakes (hundreds of species in a few hundred-thousand years), Hawaiian honeycreepers.
Key Terms
EvolutionHeritable change in the characteristics of a population over successive generations.
SpeciationThe formation of one or more new species from an existing one.
Allopatric speciationSpeciation due to geographic separation of populations.
Sympatric speciationSpeciation without geographic isolation (e.g. polyploidy, niche differentiation).
Reproductive isolationMechanisms that prevent gene flow between populations — the requirement for speciation.
Transitional fossilA fossil that shows traits intermediate between two groups (Tiktaalik, Archaeopteryx).
Homologous structureSame evolutionary origin, possibly different function — evidence of common ancestry.
Vestigial structureA reduced, non-functional remnant of an ancestral feature (e.g. whale pelvis, human coccyx).
Adaptive radiationRapid diversification from one ancestor into many species occupying different niches.
Convergent evolutionIndependent evolution of similar traits in unrelated lineages (e.g. wings in bats, birds, insects).
Divergent evolutionRelated species become more different over time as they adapt to different environments.
Prezygotic barrier HLReproductive isolation before fertilisation (temporal, behavioural, mechanical, gametic).
Postzygotic barrier HLReproductive isolation after fertilisation (hybrid inviability or sterility).
Polyploidy HLPossession of more than two complete chromosome sets; a major route to sympatric speciation in plants.
Punctuated equilibrium vs gradualism HLLong periods of stasis interrupted by short bursts of change (Eldredge & Gould) vs slow continuous change (Darwin).
Exam tip: A common essay prompt is "Outline evidence for evolution." Bring at least four lines of evidence: fossils, comparative anatomy, biogeography, and molecular/DNA. Use specific examples for each.
Practice Questions
List four independent lines of evidence for evolution.
(1) Fossil record showing transitional forms (Tiktaalik — fish-to-tetrapod). (2) Comparative anatomy — homologous structures (pentadactyl limb). (3) Biogeography — related species on neighbouring islands (Galápagos finches). (4) Molecular biology — shared DNA sequences and the universal genetic code; the same gene differs by predictable amounts in proportion to evolutionary distance.
Distinguish between allopatric and sympatric speciation, giving an example of each.
Allopatric requires geographic separation — e.g. squirrels on the north vs south rim of the Grand Canyon. Sympatric occurs without geographic barriers — e.g. cichlid fish in Lake Victoria diversified by mate preference and niche; many flowering plants form new species instantly by polyploidy.
Why are Darwin's finches a classic example of adaptive radiation?
A single ancestral seed-eating finch arrived on the Galápagos. With many empty niches (insect-eating, cactus-feeding, ground vs tree habitats) and isolated islands, populations diverged into 13 species each with a beak adapted to its food source — rapid diversification of one lineage to fill many niches.
HL How does polyploidy lead to instant sympatric speciation in plants?
An error in meiosis (or non-disjunction during mitosis after hybridisation) produces a tetraploid (4n) offspring within a diploid (2n) population. The 4n individual can self-fertilise or pair with other 4n individuals but cannot produce viable offspring with the 2n parents (3n offspring would be sterile). Thus reproductive isolation is established in a single generation. Many crop plants (wheat, cotton, strawberries) are polyploids.
HL Distinguish between prezygotic and postzygotic reproductive isolation, with one example of each.
Prezygotic: prevents fertilisation. Example — temporal isolation: two cicada species emerge in different years. Postzygotic: fertilisation occurs but offspring are inviable or sterile. Example — mule (horse × donkey) is viable but sterile due to mismatched chromosome numbers preventing normal meiosis.
D4.2 · SL + HL
7. Natural Selection
Summary
Darwin and Wallace's theory of natural selection has four logical premises: (1) populations produce more offspring than the environment can support; (2) individuals show heritable variation; (3) variation affects survival and reproduction (some variants are "fitter"); (4) over generations, advantageous variants increase in frequency. The result is adaptation — populations become better matched to their environment.
Three modes of selection act on continuous traits. Directional selection shifts the population mean in one direction (e.g. peppered moths during industrialisation, antibiotic resistance in bacteria). Stabilising selection favours intermediate phenotypes against extremes (e.g. human birth weight ~3.5 kg has lowest infant mortality). Disruptive selection favours both extremes against the intermediate (can drive sympatric speciation — e.g. African seedcrackers with two beak sizes adapted to two seed types).
Classic case studies: peppered moths (Biston betularia) — frequency of the dark carbonaria allele rose sharply during the Industrial Revolution as soot darkened tree trunks and reversed after Clean Air Acts. Antibiotic resistance in MRSA, TB and gonorrhoea — pre-existing resistance alleles are selected for whenever antibiotics are used; this is observable evolution within human lifetimes. Galápagos finches — Peter and Rosemary Grant measured average beak depth in Geospiza fortis shifting in real time in response to drought years that favoured tougher seeds.
HL The Hardy-Weinberg equilibrium describes a non-evolving population: allele frequencies stay constant if (1) no mutation, (2) no migration, (3) no selection, (4) random mating, (5) very large population (no drift). If p = frequency of the dominant allele and q = frequency of the recessive (p + q = 1), then genotype frequencies are p² + 2pq + q² = 1. Deviations from H-W indicate one or more of these forces is acting. Genetic drift is random change in allele frequencies due to sampling — most powerful in small populations (founder effect, bottleneck).
Key Terms
Natural selectionDifferential survival and reproduction of individuals due to inherited variation in fitness.
FitnessReproductive success — the number of viable offspring an individual leaves to the next generation.
AdaptationAn inherited trait that increases an organism's fitness in its environment.
Directional selectionShifts the mean phenotype toward one extreme (e.g. peppered moth, antibiotic resistance).
Stabilising selectionFavours intermediate phenotypes; reduces variance (e.g. human birth weight).
Disruptive selectionFavours both extremes against the mean; can lead to speciation.
Sexual selectionSelection for traits that increase mating success (e.g. peacock tail, antlers).
Artificial selectionSelective breeding by humans — proof of principle for natural selection (Darwin's pigeons, dog breeds).
Antibiotic resistanceBacterial evolution via natural selection on pre-existing resistance alleles when antibiotics are applied.
Allele frequencyThe proportion of one allele among all alleles for a given gene in a population.
Hardy-Weinberg equilibrium HLp² + 2pq + q² = 1. Allele frequencies stay constant in the absence of evolutionary forces.
Genetic drift HLRandom change in allele frequencies due to sampling — strongest in small populations.
Founder effect HLLoss of genetic variation when a few individuals establish a new population.
Bottleneck HLDrastic reduction in population size, randomly altering allele frequencies (e.g. cheetahs).
Exam tip: When asked to "explain natural selection", always give Darwin's four premises in order — overproduction, heritable variation, differential survival/reproduction, change in allele frequencies — and tie each to a concrete example (peppered moths or antibiotic resistance work for every IB exam).
Practice Questions
Outline the four conditions necessary for natural selection to occur.
(1) Overproduction: more offspring are produced than can survive. (2) Heritable variation: individuals differ in traits, and those differences are inherited. (3) Differential survival/reproduction: some variants survive and reproduce more than others (fitness differences). (4) Change in allele frequencies: over generations, advantageous alleles increase in the population.
Explain how antibiotic resistance arises and spreads in bacterial populations.
Random mutations occasionally produce resistance alleles in a bacterial population. When an antibiotic is applied, susceptible bacteria die but resistant ones survive and reproduce — selection acts on existing variation. Because bacteria reproduce every ~20 min and share plasmids horizontally, resistance alleles spread rapidly. Misuse of antibiotics (incomplete courses, agricultural use) intensifies this selection pressure.
Distinguish between directional, stabilising and disruptive selection, with one example of each.
Directional: mean shifts toward one extreme — peppered moth darkening during industrialisation. Stabilising: intermediate favoured, extremes selected against — human birth weight clusters around 3.5 kg. Disruptive: both extremes favoured against the middle — African black-bellied seedcrackers with two distinct beak sizes for two food sources.
Why was the peppered moth a landmark example of natural selection in action?
It was one of the first cases of natural selection observed in real time. Before the Industrial Revolution, light typica moths were camouflaged on lichen-covered trees and dominated. Industrial soot killed lichens and blackened bark; the dark carbonaria form (caused by a single mutation) became better camouflaged and its frequency rose from <2% to >95% in industrial cities within 50 years. After Clean Air Acts the frequencies reversed — confirming selection driven by predation by birds.
HL In a population, 16% of individuals are homozygous recessive for a trait. Calculate p, q, and the heterozygote frequency. Assume H-W equilibrium.
q² = 0.16, so q = 0.4. Therefore p = 1 − 0.4 = 0.6. Heterozygote frequency = 2pq = 2(0.6)(0.4) = 0.48, or 48% of the population.
HL List the five assumptions of Hardy-Weinberg equilibrium.
(1) No mutation. (2) No migration (no gene flow in or out). (3) No natural selection. (4) Random mating. (5) Very large population size (no genetic drift). Real populations almost always violate at least one — H-W is therefore used as a null model: deviations from it reveal the evolutionary forces at work.
HL Explain why genetic drift has a larger effect in small populations.
Allele frequencies change each generation by random sampling of gametes. In a large population the random fluctuations average out (law of large numbers). In a small population the random sampling error is proportionally much greater, so allele frequencies can swing dramatically — and rare alleles can be lost (or fixed) by chance alone, regardless of fitness.