Biodiversity, Classification and Evolution

Biodiversity, Classification and Evolution

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Board Coverage AQA Paper 2 | Edexcel A Paper 2 | OCR (A) Paper 2 | CIE Paper 4

1. Biodiversity

1.1 Defining Biodiversity

Definition. Biodiversity is the variety of life at every level of biological organisation: genetic diversity within species, species diversity within communities, and ecosystem diversity across landscapes.

Biodiversity encompasses three hierarchical levels:

1. Genetic diversity: the range of alleles within a population or species. High genetic diversity increases the capacity of a population to adapt to environmental change through natural selection.
2. Species diversity: the number of different species and their relative abundances in a community. This is the most commonly measured level.
3. Ecosystem diversity: the range of different habitats and ecological processes within a geographic area.

1.2 Measuring Species Diversity

Species diversity has two components:

• Species richness ($S$): the number of different species in a community.
• Species evenness: how evenly individuals are distributed among species.

A community with high richness and high evenness has higher diversity than one with high richness but low evenness (where one or a few species dominate).

1.3 Simpson's Index of Diversity

Simpson's Diversity Index ($D$) quantifies species diversity by accounting for both richness and evenness:

$D = 1 - \sum_{i=1}^{S} \frac{n_i(n_i - 1)}{N(N - 1)}$

where $S$ is the number of species, $n_i$ is the number of individuals of species $i$, and $N$ is the total number of individuals.

$D$ ranges from $0$ (no diversity: all individuals belong to a single species) to approaching $1$ (high diversity: many species, all equally abundant).

Example. Community A has 10 species each with 10 individuals ($N = 100$). Community B has 10 species with 91 individuals of one species and 1 individual of each of the other 9 ($N = 100$).

Community A: $D = 1 - 10 \times \frac◆LB◆10 \times 9◆RB◆◆LB◆100 \times 99◆RB◆ = 1 - 0.0909 = 0.909$.

Community B: $D = 1 - \left(\frac◆LB◆91 \times 90◆RB◆◆LB◆100 \times 99◆RB◆ + 9 \times \frac◆LB◆1 \times 0◆RB◆◆LB◆100 \times 99◆RB◆\right) = 1 - 0.8273 = 0.173$.

Community A has much higher diversity despite having the same species richness, because evenness is higher.

1.4 Measuring Genetic Diversity

Genetic diversity within a population can be measured by:

• Proportion of polymorphic gene loci: the fraction of gene loci that have more than one allele in the population.
• Heterozygosity: the proportion of individuals that are heterozygous at a given locus.
• Allele frequency: the proportion of each allele at a given locus in the population's gene pool.

Modern molecular techniques allow direct measurement: DNA sequencing, gel electrophoresis of proteins, and PCR-based methods to quantify allele variation.

warning

warning only one component. Simpson's Index incorporates both richness and evenness, giving a more accurate measure of diversity. A community dominated by one species with many rare species has low diversity despite high richness.

1.5 Sampling Methods

Sampling is necessary because it is impractical to count every organism. Key principles:

• Random sampling: every individual has an equal probability of being selected. Prevents bias.
• Sufficient sample size: larger samples more accurately represent the population.
• Multiple samples: replicate samples to account for spatial variation.

Techniques:

Method	Habitat	Description
Quadrat (frame or point)	Grassland, slow-moving water	A square frame of known area; count or estimate percentage cover
Transect (line or belt)	Zonation studies (e.g., seashore)	A line along which quadrats are placed at regular intervals
Sweep netting	Tall vegetation	A net swept through vegetation; captures mobile invertebrates
Pitfall trap	Ground-dwelling invertebrates	Containers sunk into the ground; organisms fall in
Kick sampling	Freshwater invertebrates	River bed disturbed upstream of a net; organisms washed into net
Light trap	Flying insects	A light source attracts phototactic insects to a collecting vessel

2. Classification

2.1 Taxonomy

Taxonomy is the science of classifying organisms into a hierarchical system based on shared characteristics and evolutionary relationships.

The traditional Linnaean hierarchy:

$\mathrm{Domain} \to \mathrm{Kingdom} \to \mathrm{Phylum} \to \mathrm{Class} \to \mathrm{Order} \to \mathrm{Family} \to \mathrm{Genus} \to \mathrm{Species}$

A species is defined by the biological species concept (Mayr, 1942): a group of interbreeding organisms that are reproductively isolated from other such groups, producing fertile offspring. Organisms are identified by binomial nomenclature: genus name (capitalised) + specific epithet (lowercase), both in italics or underlined. For example, Homo sapiens.

2.2 The Three-Domain System

Carl Woese (1990) proposed the three-domain system based on ribosomal RNA (rRNA) sequences, which revealed fundamental molecular differences between groups previously lumped together:

Domain	Cell Type	Cell Wall	Membrane Lipids	rRNA
Bacteria	Prokaryotic	Peptidoglycan	Unbranched, ester-linked	One type
Archaea	Prokaryotic	Pseudopeptidoglycan (some)	Branched, ether-linked	Distinct type
Eukarya	Eukaryotic	Cellulose (plants), chitin (fungi)	Unbranched, ester-linked	Distinct type

Archaea are more closely related to Eukarya than to Bacteria, despite their superficial similarity to bacteria.

2.3 Phylogeny and Cladistics

Phylogeny is the study of the evolutionary history and relationships among organisms. A phylogenetic tree represents these relationships as a branching diagram, where the nodes represent common ancestors and the branch lengths represent the amount of evolutionary change (usually measured in number of mutations).

Cladistics is a method of classification based purely on evolutionary relationships, grouping organisms into clades (monophyletic groups): a clade consists of an ancestral species and all of its descendants.

A cladogram is constructed by comparing homologous characteristics:

• Shared ancestral (plesiomorphic) characteristics: inherited from a distant ancestor; present in all members of the group. Not useful for distinguishing between groups.
• Shared derived (apomorphic) characteristics: evolved in a recent common ancestor; present in some but not all members. Used to define clades.

The principle of parsimony is applied: the cladogram requiring the fewest evolutionary changes is preferred.

warning

Common Pitfall Students often confuse analogous and homologous structures. Homologous structures share a common evolutionary origin (e.g., the pentadactyl limb in mammals, birds, reptiles, and amphibians). Analogous structures perform a similar function but have different evolutionary origins (e.g., the wings of insects and birds). Only homologous structures are informative for cladistics.

3. Evolution

3.1 Natural Selection

Definition. Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is the primary mechanism of adaptive evolution.

The conditions required for natural selection to operate:

1. Variation: individuals in a population must differ in their phenotypes. This variation arises from mutation, meiosis (independent assortment, crossing over), and random fertilisation.
2. Heritability: at least some of the phenotypic variation must have a genetic basis, so that it can be passed to offspring.
3. Differential fitness: some phenotypes confer a survival or reproductive advantage in a given environment. These individuals leave more offspring.

When these conditions are met, the allele frequencies in the population change over generations -- this is evolution by natural selection.

3.2 Types of Selection

Directional selection: one extreme phenotype is favoured, shifting the population mean in one direction. Example: antibiotic resistance in bacteria; industrial melanism in peppered moths during the Industrial Revolution.

Stabilising selection: intermediate phenotypes are favoured; extremes are selected against. Example: human birth weight (very low or very high birth weight is associated with higher infant mortality). This maintains the status quo and reduces variation.

Disruptive selection: both extremes are favoured over the intermediate. Example: beak size in African seedcracker finches, where large-beaked birds crack hard seeds and small-beaked birds handle soft seeds, but intermediate beaks are inefficient at both.

3.3 Speciation

Speciation is the formation of new species from pre-existing ones. It requires reproductive isolation -- the prevention of gene flow between populations.

Allopatric speciation (geographic speciation):

1. A physical barrier (mountain range, river, ocean) divides a population into two geographically isolated groups.
2. Each population experiences different selection pressures and accumulates different mutations.
3. Over time, the populations diverge genetically and phenotypically.
4. Even if the barrier is removed, the populations can no longer interbreed to produce fertile offspring -- they are separate species.

Sympatric speciation (within the same geographic area):

• Occurs without geographic separation.
• Mechanisms include: polyploidy (common in plants -- chromosome duplication creates instant reproductive isolation), behavioural isolation (different courtship displays), temporal isolation (different breeding seasons), and ecological isolation (different habitats within the same area).

Reproductive isolation mechanisms:

Pre-zygotic barriers	Post-zygotic barriers
Habitat isolation	Hybrid inviability (offspring do not survive)
Temporal isolation	Hybrid sterility (offspring are sterile, e.g., mules)
Behavioural isolation	Hybrid breakdown (second generation is inviable/sterile)
Mechanical isolation
Gametic isolation

3.4 Evidence for Evolution

• Fossil record: provides a chronological sequence of changes in organisms; transitional fossils (e.g., Archaeopteryx, Tiktaalik) show intermediate forms between groups.
• Comparative anatomy: homologous structures indicate common ancestry.
• Comparative biochemistry: the universal genetic code, shared proteins (e.g., cytochrome c), and similar metabolic pathways across all domains of life.
• Molecular evidence: DNA and protein sequences show that closely related organisms have more similar sequences; molecular clocks can estimate divergence times from mutation rates.
• Biogeography: the geographic distribution of species reflects evolutionary history (e.g., unique fauna on isolated islands such as the Galapagos and Australia).

4. Genetic Diversity

4.1 Sources of Genetic Variation

1. Mutation: the ultimate source of all new alleles. Spontaneous mutations occur at a rate of approximately $10^{-6}$ per gene per generation. Mutations include base substitutions (point mutations), insertions, deletions, and chromosomal rearrangements. Most mutations are neutral or harmful; rare beneficial mutations provide the raw material for natural selection.

2. Meiosis:

   • Crossing over (recombination): during prophase I, homologous chromosomes exchange corresponding segments, creating new combinations of alleles on the same chromosome.
   • Independent assortment: during metaphase I, the orientation of homologous chromosome pairs on the metaphase plate is random. For $n$ chromosome pairs, $2^n$ possible combinations of chromosomes in gametes.

3. Random fertilisation: any sperm can fuse with any egg, further multiplying the genetic combinations.

The total number of possible genotypic combinations from meiosis and random fertilisation in humans (23 chromosome pairs) is approximately $2^{23} \times 2^{23} \approx 7 \times 10^{13}$.

4.2 The Hardy-Weinberg Principle

The Hardy-Weinberg equilibrium describes a theoretical population in which allele frequencies do not change from generation to generation. For a gene with two alleles, $A$ and $a$, with frequencies $p$ and $q$:

$p + q = 1$

$p^2 + 2pq + q^2 = 1$

where $p^2$ = frequency of genotype $AA$, $2pq$ = frequency of genotype $Aa$, $q^2$ = frequency of genotype $aa$.

Conditions for Hardy-Weinberg equilibrium:

• No mutations
• No selection (all genotypes have equal fitness)
• Random mating
• No migration (no gene flow)
• Very large population size (no genetic drift)

Real populations rarely meet all these conditions. The principle is useful as a null model: if observed genotype frequencies deviate from H-W predictions, one of the conditions is violated, suggesting that evolution is occurring.

Example. In a population of 500 individuals, 320 are homozygous dominant ($AA$), 160 are heterozygous ($Aa$), and 20 are homozygous recessive ($aa$).

Total alleles: $N = 2 \times 500 = 1000$. Frequency of $a$: $q = \frac◆LB◆(2 \times 20) + 160◆RB◆◆LB◆1000◆RB◆ = \frac{200}{1000} = 0.2$. Frequency of $A$: $p = 1 - 0.2 = 0.8$. Expected under H-W: $p^2 = 0.64$ ($320$ individuals), $2pq = 0.32$ ($160$ individuals), $q^2 = 0.04$ ($20$ individuals). The observed frequencies match H-W predictions, suggesting the population is approximately in equilibrium.

warning

Common Pitfall Students sometimes think Hardy-Weinberg equilibrium means no evolution is occurring. It describes the theoretical conditions under which allele frequencies remain constant. If a population deviates from H-W, this is evidence that evolutionary forces (selection, drift, gene flow, mutation, non-random mating) are acting.

5. Genetic Drift and Gene Flow

5.1 Genetic Drift

Genetic drift is the random fluctuation of allele frequencies from generation to generation due to chance events in the sampling of gametes. Its effect is inversely proportional to population size: drift is strong in small populations and negligible in large ones.

The bottleneck effect: a sharp reduction in population size (due to natural disaster, hunting, habitat destruction) drastically reduces genetic diversity. The surviving population may have allele frequencies very different from the original population, purely by chance. Even if the population recovers in size, the reduced genetic diversity persists.

Quantitative example. A population of 1000 individuals has an allele frequency $p = 0.5$ for allele $A$. A bottleneck reduces the population to 10 individuals. By chance, only 2 of the survivors carry allele $A$, so the new frequency is $p = 2/20 = 0.1$ (assuming diploid). The population has lost 80% of the $A$ allele frequency purely through drift. Recovery of the population to its original size will not restore the lost alleles.

The founder effect: a small number of individuals colonise a new area, carrying only a subset of the genetic variation of the source population. The founder population may have very different allele frequencies. This is a form of genetic drift and explains the high frequency of certain genetic disorders in isolated populations (e.g., Ellis-van Creveld syndrome among the Amish, or Huntington's disease in the Lake Maracaibo region of Venezuela).

5.2 Gene Flow

Gene flow (migration) is the movement of alleles between populations through the movement of individuals or gametes (e.g., pollen dispersal). Gene flow tends to reduce genetic differences between populations and counteracts the effects of natural selection and drift. If gene flow is extensive, populations remain genetically similar. If gene flow is prevented (by a geographic barrier), populations diverge and may eventually become separate species.

5.3 Comparing Evolutionary Mechanisms

Mechanism	Direction of Change	Speed	Role in Evolution
Natural selection	Directional (towards fitness)	Slow-moderate	Adaptation to environment
Genetic drift	Random	Variable	Loss of diversity; fixation
Gene flow	Homogenising (between populations)	Variable	Prevents speciation
Mutation	Random (new alleles)	Very slow	Source of new variation

warning

Common Pitfall Students often think that evolution always leads to "improvement" or "progress." Natural selection produces adaptations to the current environment, not to some absolute standard of fitness. What is advantageous in one environment may be disadvantageous in another. Genetic drift produces changes without regard to fitness at all.

6. Molecular Clocks and Phylogenetics

6.1 The Molecular Clock Concept

If mutations accumulate in DNA at a roughly constant rate, the number of sequence differences between two species is proportional to the time since they diverged from a common ancestor. This is the molecular clock hypothesis.

The mutation rate per site per year ($\mu$) is estimated by calibrating the clock against the fossil record. For example, if two species diverged from a common ancestor 10 million years ago (as determined by fossils) and their DNA sequences now differ at 2% of sites, the mutation rate is estimated as:

$\mu = \frac◆LB◆0.02◆RB◆◆LB◆2 \times 10^7\ \mathrm{years}◆RB◆ = 1 \times 10^{-9}\ \mathrm{mutations\ per\ site\ per\ year}$

The factor of 2 accounts for the fact that both lineages have been accumulating mutations independently since divergence.

6.2 Worked Example: Estimating Divergence Time

The cytochrome c gene differs by 12 nucleotide substitutions between species X and species Y. The accepted mutation rate for this gene is $\mu = 2.5 \times 10^{-9}$ substitutions per site per year. The gene is 330 base pairs long.

Number of substitutions per site $= \frac{12}{330} = 0.0364$.

Time since divergence $= \frac◆LB◆0.0364◆RB◆◆LB◆2 \times 2.5 \times 10^{-9}◆RB◆ = 7.27 \times 10^6\ \mathrm{years} \approx 7.3\ \mathrm{million\ years}$.

6.3 Limitations of Molecular Clocks

The molecular clock assumption of constant mutation rate is an approximation. In reality:

• Mutation rates vary between genes (non-coding DNA mutates faster than coding DNA due to weaker selective constraint).
• Mutation rates vary between lineages (organisms with shorter generation times accumulate mutations faster).
• Natural selection can accelerate or decelerate the rate of sequence change.
• Different genes give different estimates of divergence time.

Despite these limitations, molecular clocks provide useful approximate dates, especially when combined with fossil evidence.

7. Advanced Hardy-Weinberg Calculations

7.1 Multiple Alleles

When a gene has more than two alleles, the Hardy-Weinberg principle is extended. For three alleles with frequencies $p$, $q$, and $r$:

$p + q + r = 1$

$p^2 + q^2 + r^2 + 2pq + 2pr + 2qr = 1$

Worked Example. The ABO blood group system has three alleles: $I^A$, $I^B$, and $i$. Their frequencies in a population are $p = 0.3$, $q = 0.1$, $r = 0.6$.

Genotype frequencies:

• $I^AI^A$: $p^2 = 0.09$ (blood group A)
• $I^AI^B$: $2pq = 0.06$ (blood group AB)
• $I^Ai$: $2pr = 0.36$ (blood group A)
• $I^Bi^B$: $q^2 = 0.01$ (blood group B)
• $I^Bi$: $2qr = 0.12$ (blood group B)
• $ii$: $r^2 = 0.36$ (blood group O)

Phenotype frequencies:

• Blood group A: $p^2 + 2pr = 0.09 + 0.36 = 0.45$
• Blood group B: $q^2 + 2qr = 0.01 + 0.12 = 0.13$
• Blood group AB: $2pq = 0.06$
• Blood group O: $r^2 = 0.36$

Check: $0.45 + 0.13 + 0.06 + 0.36 = 1.00$. $\square$

7.2 Testing for Hardy-Weinberg Equilibrium: The Chi-Squared Test

When observed genotype frequencies are given, the chi-squared test determines whether deviations from H-W predictions are statistically significant.

$\chi^2 = \sum \frac{(O - E)^2}{E}$

where $O$ = observed frequency and $E$ = expected frequency under H-W.

Degrees of freedom for a gene with $n$ alleles: $\mathrm{df} = \frac{n(n+1)}{2} - 1 - k$, where $k$ is the number of allele frequencies estimated from the data. For a two-allele system where both $p$ and $q$ are estimated: $\mathrm{df} = 3 - 1 - 1 = 1$.

Worked Example. In a population of 1000, the observed genotypes for a two-allele system are: $AA = 420$, $Aa = 400$, $aa = 180$.

Step 1: Calculate allele frequencies from observed data.

$p = \frac{2(420) + 400}{2(1000)} = \frac{1240}{2000} = 0.62$

$q = 1 - 0.62 = 0.38$

Step 2: Calculate expected frequencies.

$AA$: $p^2 = 0.3844$, expected $= 384.4$

$Aa$: $2pq = 0.4712$, expected $= 471.2$

$aa$: $q^2 = 0.1444$, expected $= 144.4$

Step 3: Calculate $\chi^2$.

$\chi^2 = \frac{(420 - 384.4)^2}{384.4} + \frac{(400 - 471.2)^2}{471.2} + \frac{(180 - 144.4)^2}{144.4}$

$= \frac{1267.36}{384.4} + \frac{5067.84}{471.2} + \frac{1267.36}{144.4}$

$= 3.30 + 10.76 + 8.78 = 22.84$

Degrees of freedom $= 1$. Critical value at $p = 0.05$ for 1 df is $3.84$.

Since $\chi^2 = 22.84 \gg 3.84$, we reject the null hypothesis. The population is not in Hardy-Weinberg equilibrium. Possible explanations include non-random mating, selection against one genotype, or population substructure (Wahlund effect).

warning

Common Pitfall When calculating degrees of freedom for the chi-squared test with Hardy-Weinberg data, students often incorrectly use $\mathrm{df} = n - 1$ (where $n$ is the number of genotypes). The correct formula accounts for the fact that allele frequencies are estimated from the data, reducing the degrees of freedom further. For a two-allele system, $\mathrm{df} = 1$.

8. Classification: The Five Kingdom System and Beyond

8.1 Whittaker's Five-Kingdom System

Before the three-domain system, organisms were classified into five kingdoms (Whittaker, 1969):

Kingdom	Cell Type	Nuclear Envelope	Nutrition
Animalia	Eukaryotic	Present	Heterotrophic (ingestive)
Plantae	Eukaryotic	Present	Autotrophic (photosynthetic)
Fungi	Eukaryotic	Present	Heterotrophic (absorptive)
Protoctista	Eukaryotic	Present	Mixed (autotrophic/heterotrophic)
Prokaryota	Prokaryotic	Absent	Various

The five-kingdom system was superseded because it placed all prokaryotes in a single kingdom, despite the profound molecular differences between Bacteria and Archaea revealed by rRNA sequencing. The three-domain system (Woese, 1990) better reflects evolutionary relationships.

8.2 Courtship Behaviour as a Reproductive Isolating Mechanism

Courtship behaviours are species-specific rituals that serve two functions:

1. Species recognition: ensuring mating occurs between members of the same species, preventing wasted reproductive effort and hybrid offspring with reduced fitness.
2. Mate selection: allowing individuals to assess the quality, health, and fitness of potential partners.

Courtship behaviour is a pre-zygotic reproductive barrier. If courtship signals are not recognised or responded to correctly, mating does not occur. Examples: the complex courtship dance of the blue-footed booby; the specific song patterns of crickets and birds; chemical pheromone signals in moths.

Courtship behaviours evolve through sexual selection and can drive speciation: if a population is divided and courtship rituals diverge (e.g., through mutation or cultural drift), the two subpopulations may become reproductively isolated even without geographic separation (sympatric speciation by behavioural isolation).

Practice Problems

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Problem 1

Calculate Simpson's Diversity Index for a community with the following species abundances:

Species A: 45, Species B: 30, Species C: 15, Species D: 8, Species E: 2.

Answer. $N = 45 + 30 + 15 + 8 + 2 = 100$.

$D = 1 - \left(\frac◆LB◆45 \times 44◆RB◆◆LB◆100 \times 99◆RB◆ + \frac◆LB◆30 \times 29◆RB◆◆LB◆100 \times 99◆RB◆ + \frac◆LB◆15 \times 14◆RB◆◆LB◆100 \times 99◆RB◆ + \frac◆LB◆8 \times 7◆RB◆◆LB◆100 \times 99◆RB◆ + \frac◆LB◆2 \times 1◆RB◆◆LB◆100 \times 99◆RB◆\right)$

$= 1 - (0.2000 + 0.0879 + 0.0212 + 0.0006 + 0.0002)$

$= 1 - 0.3099 = 0.690$.

The index value of $0.69$ indicates moderate diversity. The community is dominated by Species A, which reduces the evenness component.

If you get this wrong, revise: Simpson's Index of Diversity

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Problem 2

In a population of snapdragons, the allele for red flowers ($R$) is incompletely dominant over the allele for white flowers ($W$). Heterozygotes ($RW$) are pink. In a population of 1000 plants, 640 are red, 200 are pink, and 160 are white. Use the Hardy-Weinberg principle to calculate the allele frequencies and determine whether the population is in equilibrium.

Answer. Total alleles: $N = 2000$.

Frequency of $R$: $p = \frac◆LB◆(2 \times 640) + 200◆RB◆◆LB◆2000◆RB◆ = \frac{1480}{2000} = 0.74$.

Frequency of $W$: $q = \frac◆LB◆(2 \times 160) + 200◆RB◆◆LB◆2000◆RB◆ = \frac{520}{2000} = 0.26$.

Expected genotype frequencies under H-W: $p^2 = 0.5476$ ($548$ red), $2pq = 0.3848$ ($385$ pink), $q^2 = 0.0676$ ($68$ white).

Observed: 640 red, 200 pink, 160 white. The observed values differ substantially from expected (e.g., 640 vs. 548 red; 160 vs. 68 white), indicating the population is not in Hardy-Weinberg equilibrium. This suggests selection is acting against the white homozygote or in favour of the red homozygote.

If you get this wrong, revise: The Hardy-Weinberg Principle

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Problem 3

Explain the difference between allopatric and sympatric speciation, giving an example of each.

Answer. Allopatric speciation occurs when a geographical barrier physically separates a population into two groups, preventing gene flow. Each group experiences different selection pressures and accumulates different mutations independently. Over many generations, the populations diverge until they are reproductively isolated. Example: the Kaibab squirrel and Abert's squirrel were separated by the Grand Canyon and have evolved into distinct species. Sympatric speciation occurs without geographic separation. Example: polyploidy in plants -- a mutation causes chromosome duplication, producing an individual with four sets of chromosomes. This individual can self-fertilise or reproduce with other polyploid individuals, but cannot interbreed with the original diploid population, creating instant reproductive isolation and a new species.

If you get this wrong, revise: Speciation

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Problem 4

A researcher studying a population of 200 beetles finds that 18 are homozygous recessive for a gene causing striped wings ($aa$). Calculate the frequency of the recessive allele, the dominant allele, and the number of heterozygous beetles.

Answer. $q^2 = 18/200 = 0.09$, so $q = \sqrt{0.09} = 0.3$.

$p = 1 - q = 1 - 0.3 = 0.7$.

Frequency of heterozygotes: $2pq = 2 \times 0.7 \times 0.3 = 0.42$.

Number of heterozygous beetles: $0.42 \times 200 = 84$.

Check: $p^2 = 0.49$ ($98$ individuals), $2pq = 0.42$ ($84$ individuals), $q^2 = 0.09$ ($18$ individuals). Total $= 98 + 84 + 18 = 200$. $\square$

If you get this wrong, revise: The Hardy-Weinberg Principle

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Problem 5

Explain how the overuse of antibiotics has led to the evolution of antibiotic-resistant bacteria. Use the concepts of variation, selection, and inheritance in your answer.

Answer. Within any bacterial population, random mutations generate genetic variation. A small number of bacteria may carry mutations that confer resistance to a particular antibiotic. When the antibiotic is applied, susceptible bacteria are killed (strong selective pressure), but resistant bacteria survive and reproduce. Because bacteria reproduce asexually by binary fission, the resistance allele is passed to all offspring. The resistant population grows rapidly, and the antibiotic becomes ineffective. The overuse of antibiotics (e.g., prescribing them for viral infections, incomplete courses, use in livestock) increases the selective pressure, accelerating the evolution of resistance. This is directional selection: the phenotype for resistance is strongly favoured, shifting the allele frequency in the population.

If you get this wrong, revise: Natural Selection

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Problem 6

Explain why cladistics is considered a more scientifically rigorous classification system than traditional Linnaean taxonomy.

Answer. Traditional Linnaean taxonomy classifies organisms based on overall morphological similarity, which can be misleading because convergent evolution can produce analogous structures (similar function, different origin). Cladistics is based purely on shared derived characteristics (homologous traits) that indicate common ancestry, identified through molecular and morphological analysis. Cladistic classification produces monophyletic groups (clades) where every member shares a common ancestor not shared with any member outside the group. This is objective, testable, and consistent with the theory of evolution. Linnaean taxonomy sometimes produces paraphyletic groups (groups that include a common ancestor but not all descendants), which are not evolutionarily meaningful. The use of molecular data (DNA/RNA sequences) in cladistics provides quantitative measures of evolutionary distance, allowing precise estimation of divergence times and relationships.

If you get this wrong, revise: Phylogeny and Cladistics

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Problem 7

A population of 1000 individuals of a flowering plant has the following genotype frequencies for a gene with two alleles ($F$ and $f$): $FF = 490$, $Ff = 420$, $ff = 90$. (a) Calculate the allele frequencies. (b) Use the chi-squared test to determine whether the population is in Hardy-Weinberg equilibrium. (c) Suggest a possible biological explanation if the population is not in equilibrium.

Answer. (a) Total alleles $= 2000$.

$p = \frac{2(490) + 420}{2000} = \frac{1400}{2000} = 0.70$.

$q = \frac{2(90) + 420}{2000} = \frac{600}{2000} = 0.30$.

(b) Expected frequencies: $p^2 = 0.49$ ($490$), $2pq = 0.42$ ($420$), $q^2 = 0.09$ ($90$).

$\chi^2 = \frac{(490 - 490)^2}{490} + \frac{(420 - 420)^2}{420} + \frac{(90 - 90)^2}{90} = 0$.

Degrees of freedom $= 1$. Since $\chi^2 = 0 < 3.84$, the population is in perfect Hardy-Weinberg equilibrium. No evolutionary forces are detectably acting on this gene.

(c) Not applicable in this case -- the population is in equilibrium. However, if the chi-squared value had been significant, possible explanations would include: selection favouring the heterozygote (heterozygote advantage), non-random mating (assortative mating or inbreeding), or population substructure (the Wahlund effect).

If you get this wrong, revise: The Hardy-Weinberg Principle and Advanced Hardy-Weinberg Calculations

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Problem 8

Two species of finch live on the same island. Species A has a large, strong beak and feeds on hard seeds. Species B has a small, slender beak and feeds on small seeds and insects. (a) Explain how resource partitioning allows these two species to coexist. (b) A drought kills all plants that produce small seeds, leaving only hard-seeded plants. Predict the effect on each species and explain in terms of natural selection. (c) After the drought, a hybrid individual is observed with an intermediate beak size. Explain why this hybrid is likely to have reduced fitness.

Answer. (a) The two species exploit different food resources (resource partitioning), reducing direct competition. Species A specialises in hard seeds (which Species B cannot crack), and Species B specialises in small seeds and insects (which Species A handles inefficiently). This allows both species to occupy the same habitat without violating the competitive exclusion principle.

(b) The drought eliminates the food source of Species B (small seeds and possibly the insects that depend on small-seed plants). Species B will decline due to starvation (strong directional selection against its small-beaked phenotype). Species A, which feeds on hard seeds, is unaffected by the loss of small seeds and may increase as competition from Species B is reduced.

(c) The hybrid with an intermediate beak size would be poorly adapted to either food source: the beak is too small to efficiently crack hard seeds (the only food remaining), and the small seeds and insects are no longer available. This is an example of disruptive selection: the intermediate phenotype has lower fitness than either extreme, reinforcing the divergence between the two species.

If you get this wrong, revise: Types of Selection and Natural Selection

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Problem 9

Explain how the analysis of DNA sequences can be used to construct a phylogenetic tree. In your answer, describe the role of homologous genes, molecular clocks, and the principle of parsimony.

Answer. To construct a phylogenetic tree from DNA sequences, homologous genes (genes shared by common descent, such as cytochrome c or ribosomal RNA genes) are sequenced from each species of interest. The sequences are aligned, and the number of nucleotide differences between each pair of species is counted. Species with fewer differences are more closely related (they diverged more recently). A molecular clock can be used to estimate the actual time of divergence if the mutation rate for the gene is known and has been calibrated against the fossil record. The tree is then constructed using the principle of parsimony: the tree requiring the fewest evolutionary changes (the simplest explanation) is preferred. Alternatively, maximum likelihood or Bayesian methods may be used for more sophisticated analysis. The resulting tree shows the evolutionary relationships as a branching diagram, where each node represents a common ancestor and branch lengths are proportional to the amount of genetic change.

If you get this wrong, revise: Phylogeny and Cladistics and Molecular Clocks and Phylogenetics

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9. Speciation: Detailed Mechanisms

9.1 Pre-zygotic Reproductive Barriers

Pre-zygotic barriers prevent mating or fertilisation between species:

Barrier Type	Description	Example
Temporal isolation	Species breed at different times of year or day	Bufo americanus and Bufo fowleri (toads) breed in different seasons
Habitat isolation	Species live in different habitats within the same area	Gartenmeister and Ensatina salamanders in California
Behavioural isolation	Different courtship displays or mating calls prevent interbreeding	Bird songs; firefly flash patterns
Mechanical isolation	Physical incompatibility of reproductive structures	Lock-and-key mechanism in insect genitalia
Gametic isolation	Gametes fail to fuse or are chemically incompatible	Sea urchin sperm bind to species-specific receptors on the egg jelly coat

9.2 Post-zygotic Reproductive Barriers

Post-zygotic barriers reduce the fitness of hybrid offspring:

Barrier Type	Description	Example
Hybrid inviability	Zygote fails to develop or offspring is weak/unviable	Cross between sheep and goat; embryo dies early
Hybrid sterility	Offspring are healthy but sterile	Mule (horse $\times$ donkey); 63 chromosomes (cannot pair in meiosis)
Hybrid breakdown	First-generation hybrids are fertile, but second-generation (F2) are sterile or weak	Cross between rice cultivars

9.3 Allopatric Speciation: The Model

Allopatric speciation occurs in stages:

1. Geographic isolation: a physical barrier (mountain range, river, ocean) splits a population into two subpopulations.
2. Different selection pressures: the two subpopulations experience different environments, leading to different selective pressures and different allele frequency changes.
3. Genetic drift: in small subpopulations, random changes in allele frequencies occur independently in each population.
4. Mutation: new mutations arise independently in each population.
5. Accumulation of differences: over many generations, the two populations accumulate enough genetic differences that they can no longer interbreed to produce fertile offspring. They are now separate species.

The time required for allopatric speciation varies greatly. It can occur rapidly (hundreds of generations) for organisms with short generation times and strong selection, or slowly (millions of years) for organisms with long generation times and weak selection.

9.4 Ring Species

A ring species provides direct evidence that speciation can occur through geographic isolation with gradual divergence. In a ring species, populations are distributed around a geographic barrier (e.g., a mountain range). Adjacent populations can interbreed, but populations at the two ends of the "ring" (where they meet) cannot interbreed despite being connected by a chain of interbreeding populations.

Example: Ensatina salamanders in California. Populations form a ring around the Central Valley. Adjacent populations interbreed, but where the two ends of the ring meet in Southern California, they behave as separate species (do not interbreed).

10. Taxonomy and Classification Systems

10.1 The Three-Domain System

Carl Woese (1990) proposed the three-domain system based on ribosomal RNA (rRNA) sequences:

Domain	Cell Type	Membrane Lipids	Cell Wall	Examples
Bacteria	Prokaryotic	Ester-linked, unbranched	Peptidoglycan	E. coli, Bacillus
Archaea	Prokaryotic	Ether-linked, branched (isoprene chains)	Pseudopeptidoglycan (some)	Methanobacterium, Halobacterium
Eukarya	Eukaryotic	Ester-linked, unbranched	Cellulose (plants), chitin (fungi), none (animals)	Animals, plants, fungi, protists

Archaea were originally classified with bacteria (as "archaebacteria") but rRNA sequencing showed they are as different from bacteria as bacteria are from eukaryotes. Archaea share some features with eukaryotes (e.g., histone-like proteins, similar RNA polymerase, similar translation initiation factors) despite being prokaryotic.

10.2 Classification Hierarchies

The full taxonomic hierarchy (broadest to most specific):

Domain $\to$ Kingdom $\to$ Phylum $\to$ Class $\to$ Order $\to$ Family $\to$ Genus $\to$ Species

Binomial nomenclature (two-part naming system devised by Linnaeus):

• Genus name: capitalised, e.g., Homo
• Species name: lowercase, e.g., sapiens
• Both italicised (or underlined if handwritten): Homo sapiens

10.3 Phylogenetic vs Phenetic Classification

Feature	Phylogenetic Classification	Phenetic (Numerical) Classification
Basis	Evolutionary relationships (common ancestry)	Overall similarity (morphological, biochemical)
Method	Cladistics (shared derived characteristics)	Numerical taxonomy (many characteristics scored and analysed by computer)
Groups	Monophyletic (ancestor + all descendants)	May include paraphyletic groups
Example	Birds grouped with reptiles (both are diapsids)	Birds as a separate class from reptiles (due to their distinct morphology)

Phylogenetic classification is now the preferred approach because it reflects evolutionary history, which is the fundamental organising principle of biology.

11. Biodiversity Measurement: Advanced Techniques

11.1 Species Richness vs Species Evenness

Species richness is the number of different species in a habitat. It is a simple count and does not account for the relative abundance of each species.

Species evenness (equitability) describes how evenly individuals are distributed among the species. A community where all species have similar abundances has high evenness; a community dominated by one or a few species has low evenness.

Two communities can have the same species richness but different diversity if their evenness differs:

• Community A: 4 species, 25 individuals each (high evenness, high diversity).
• Community B: 4 species, 94, 2, 2, 2 individuals (low evenness, lower effective diversity).

11.2 Simpson's Index of Diversity

$D = 1 - \frac◆LB◆\sum n(n-1)◆RB◆◆LB◆N(N-1)◆RB◆$

Where $n$ = number of individuals of each species, $N$ = total number of individuals.

$D$ ranges from 0 (no diversity, all individuals are the same species) to (almost) 1 (maximum diversity, infinite species all with equal abundance).

11.3 Worked Example: Comparing Two Habitats

Habitat 1 (managed grassland):

Species	Number ($n$)	$n(n-1)$
Grass A	40	1560
Grass B	30	870
Clover	15	210
Dandelion	10	90
Thistle	5	20
Total ($N$)	100	2750

$D_1 = 1 - \frac◆LB◆2750◆RB◆◆LB◆100 \times 99◆RB◆ = 1 - \frac{2750}{9900} = 1 - 0.278 = 0.722$

Habitat 2 (wildflower meadow):

Species	Number ($n$)	$n(n-1)$
Species A	12	132
Species B	11	110
Species C	10	90
Species D	9	72
Species E	8	56
Species F	8	56
Species G	7	42
Species H	7	42
Species I	6	30
Species J	6	30
Species K	6	30
Species L	5	20
Species M	5	20
Total ($N$)	100	730

$D_2 = 1 - \frac◆LB◆730◆RB◆◆LB◆100 \times 99◆RB◆ = 1 - \frac{730}{9900} = 1 - 0.074 = 0.926$

The wildflower meadow (Habitat 2) has higher diversity ($D = 0.926$) than the managed grassland (Habitat 1, $D = 0.722$) because it has higher species richness and greater evenness.

12. Evidence for Evolution

12.1 Palaeontology

The fossil record provides direct evidence of evolutionary change over time:

• Stratigraphy: fossils in deeper (older) rock layers are progressively different from those in shallower (younger) layers, showing gradual change.
• Transitional fossils: fossils showing intermediate features between groups (e.g., Archaeopteryx -- dinosaur-like skeleton with feathered wings, linking dinosaurs and birds; Tiktaalik -- fish-like with limb bones, linking fish and tetrapods).
• Extinction: the fossil record shows mass extinctions (e.g., Cretaceous-Paleogene extinction, 66 million years ago, which eliminated non-avian dinosaurs), followed by adaptive radiation of surviving groups.

12.2 Comparative Anatomy

Homologous structures: structures with similar anatomy and embryological origin but different functions, indicating common ancestry (e.g., the pentadactyl limb in humans, bats, whales, and horses -- all have the same basic bone arrangement but different modifications for grasping, flying, swimming, and running).

Analogous structures: structures with similar function but different anatomy and embryological origin, indicating convergent evolution (e.g., wings of insects, birds, and bats -- all used for flight but structurally very different).

Vestigial structures: remnants of structures that were functional in ancestral species but have lost their function (e.g., the human appendix, pelvic bones in whales, hind limb buds in python embryos).

12.3 Molecular Evidence

Comparing DNA and protein sequences between species provides quantitative evidence for evolution:

• Species with more similar DNA sequences are more closely related.
• Cytochrome c is a highly conserved protein (changes slowly) and is used to compare distantly related species.
• Mitochondrial DNA evolves rapidly (due to a high mutation rate and lack of histone protection) and is used to compare closely related species and populations.
• Molecular clocks: the rate of molecular change is approximately constant for a given gene, allowing the time of divergence between species to be estimated.

12.4 Biogeography

The geographic distribution of species provides evidence for evolution:

• Species on oceanic islands are most similar to species on the nearest mainland (e.g., Darwin's finches on the Galapagos Islands are related to South American finches).
• Australia's unique fauna (marsupials) reflects its long geographic isolation after the breakup of Gondwana.
• Convergent evolution produces similar adaptations in geographically separated but ecologically similar environments (e.g., cacti in the Americas and euphorbias in Africa -- both are succulent, spiny plants adapted to arid conditions, but belong to different families).

13. Hardy-Weinberg Extended: Population-Level Calculations

13.1 Testing for Selection at a Single Locus

Worked Example. In a population of snails, shell colour is determined by a single gene with two alleles: $B$ (brown, dominant) and $b$ (yellow, recessive). The population is sampled over two years:

Year	$BB$	$Bb$	$bb$	Total	$p$ ($B$)	$q$ ($b$)
1	360	480	160	1000	0.60	0.40
2	324	432	144	900	0.60	0.40

The allele frequencies have not changed ($p = 0.60$, $q = 0.40$ in both years). The population appears to be in Hardy-Weinberg equilibrium.

Chi-squared test: expected values in Year 2 based on H-W: $p^2 \times 900 = 324$ ($BB$), $2pq \times 900 = 432$ ($Bb$), $q^2 \times 900 = 144$ ($bb$). These match the observed exactly, confirming H-W equilibrium.

Now suppose Year 3 shows:

Year 3	$BB$	$Bb$	$bb$	Total
Observed	200	400	300	900

$p' = \frac{2(200) + 400}{1800} = \frac{800}{1800} = 0.444$. $q' = 0.556$.

The frequency of $b$ has increased from 0.40 to 0.556. This could indicate selection against brown shells (perhaps brown shells are more visible to predators on a light background), or genetic drift.

13.2 Selection Against a Dominant Allele

Selection against a dominant allele is very efficient because all individuals with the allele express the phenotype (both homozygous dominant and heterozygous) and are exposed to selection.

If the dominant allele $A$ is lethal ($w = 0$), then only $aa$ individuals survive. In one generation, the frequency of $a$ goes to 1.0 and the dominant allele is eliminated.

If the dominant allele has reduced fitness ($0 < w < 1$), it is eliminated more slowly but still much faster than a recessive allele with the same selection coefficient.

13.3 Migration and Allele Frequencies

Worked Example. A mainland population has allele frequency $p_m = 0.80$ for allele $A$. An island population has allele frequency $p_i = 0.20$. Migration rate from mainland to island is 10% per generation (i.e., 10% of the island population are immigrants from the mainland).

New allele frequency on the island after migration:

$p_i' = (1 - m) \times p_i + m \times p_m = 0.90 \times 0.20 + 0.10 \times 0.80 = 0.18 + 0.08 = 0.26$

After one generation of migration, the island allele frequency has changed from 0.20 to 0.26. Continued migration will gradually shift the island population towards the mainland allele frequency.

14. Adaptations: Detailed Examples

14.1 Anatomical, Physiological, and Behavioural Adaptations

Type	Definition	Example
Anatomical (structural)	Physical features of the organism	Thick insulating blubber in polar bears; counter-current heat exchange in whale flippers
Physiological (biochemical)	Internal processes	Antifreeze proteins in Antarctic fish; concentrated urine in desert kangaroo rats; anaerobic metabolism in diving mammals
Behavioural	Actions or responses of the organism	Migration in wildebeest; hibernation in hedgehogs; burrowing in meerkats

14.2 Xerophytic Adaptations

Xerophytes are plants adapted to dry environments (deserts, sand dunes):

Adaptation	Function
Thick waxy cuticle	Reduces water loss by evaporation from the epidermis
Sunken stomata	Creates a microclimate of humid air around the stomata, reducing the water vapour concentration gradient
Hairy leaves	Trap a layer of moist air around the leaf, reducing transpiration
Rolled leaves	Protects the stomata on the lower surface; creates a humid microclimate (e.g., marram grass)
Reduced leaf surface area	Fewer stomata; smaller area for water loss (e.g., cactus spines are modified leaves)
Thick palisade mesophyll	Multiple layers of palisade cells maximise photosynthesis per unit leaf area
Succulence	Thick, fleshy stems or leaves that store water (e.g., cacti, aloe)
Deep or extensive root systems	Deep taproots reach water table; widespread shallow roots capture brief rainfall

14.3 Hydrophytic Adaptations

Hydrophytes are plants adapted to living in water:

Adaptation	Function
No waxy cuticle (or very thin)	Water is not limiting; no need to reduce water loss
Stomata only on upper surface	Lower surface is submerged; gas exchange must occur above water
Air spaces (aerenchyma) in tissues	Provide buoyancy; allow gas diffusion to submerged parts
Reduced xylem	Water transport is less critical; support provided by water
Flexible stems	Bend with water current rather than breaking

15. Conservation Strategies: Case Studies

15.1 The CITES Convention

CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora, 1975) regulates international trade in species threatened with extinction:

• Appendix I: species threatened with extinction; trade is permitted only in exceptional circumstances (e.g., scientific research). Examples: all great apes, giant panda, Asian elephant, hawksbill sea turtle.
• Appendix II: species not necessarily threatened with extinction but whose trade must be controlled to avoid overexploitation. Examples: African elephant (some populations), many orchid species.
• Appendix III: species protected by individual countries that have asked other CITES parties for assistance in controlling trade.

15.2 The Rio Convention (1992)

The Convention on Biological Diversity (CBD, Earth Summit, Rio de Janeiro, 1992) established three main goals:

1. Conservation of biological diversity: protecting species, habitats, and ecosystems.
2. Sustainable use of biological resources: using resources in a way that does not deplete them.
3. Fair and equitable sharing of benefits: ensuring that the benefits from genetic resources (e.g., pharmaceutical compounds derived from rainforest plants) are shared with the countries of origin.

15.3 Managing Conservation: Role of Governments and NGOs

Organisation	Role
IUCN (International Union for Conservation of Nature)	Publishes the Red List of threatened species; defines conservation categories (extinct, critically endangered, endangered, vulnerable, near threatened, least concern)
UNEP-WCMC (UN Environment Programme World Conservation Monitoring Centre)	Maintains databases on species, habitats, and protected areas
National governments	Designate protected areas (national parks, SSSIs, nature reserves); enforce environmental legislation (Wildlife and Countryside Act 1981, UK); set fishing quotas, pollution limits
NGOs (e.g., WWF, RSPB, BirdLife International)	Purchase and manage reserves; conduct research; lobby governments; public education and fundraising
Zoos and botanical gardens	Captive breeding programmes; seed banks; public education; research

16. Advanced Classification: The Six Kingdom System

Some biologists prefer a six-kingdom system that separates bacteria and archaea:

Kingdom	Cell Type	Nutrition	Examples
Eubacteria	Prokaryotic	Various (autotrophic, heterotrophic, parasitic)	E. coli, Bacillus, Cyanobacteria
Archaebacteria (Archaea)	Prokaryotic	Various (methanogens, halophiles, thermophiles)	Methanobacterium, Halobacterium
Protista	Eukaryotic	Various (autotrophic, heterotrophic, mixotrophic)	Amoeba, Paramecium, Chlorella, Plasmodium
Fungi	Eukaryotic	Heterotrophic (absorptive)	Saccharomyces, Penicillium, Agaricus
Plantae	Eukaryotic	Autotrophic (photosynthetic)	Mosses, ferns, conifers, flowering plants
Animalia	Eukaryotic	Heterotrophic (ingestive)	Invertebrates, fish, amphibians, reptiles, birds, mammals

16.1 Difficulties in Classification

Problem	Description	Example
Ring species	Where to draw the species boundary?	Ensatina salamanders
Asexual reproduction	Biological species concept cannot be applied (no interbreeding)	Bacteria, some plants, some insects
Horizontal gene transfer	Genes are exchanged between species, blurring evolutionary boundaries	Bacteria (antibiotic resistance genes transferred between species)
Convergent evolution	Similar structures evolved independently, making classification by morphology misleading	Analogous structures (wings of bats and birds)
Extinct organisms	Only fossil evidence available; incomplete information	Dinosaurs, trilobites

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17. Natural Selection in Action: Detailed Examples

17.1 Peppered Moth (Biston betularia)

Background: Before the Industrial Revolution in England (pre-1850), the majority of peppered moths were light-coloured (typica form), with a small number of dark (carbonaria) forms. The light form was better camouflaged against lichen-covered trees.

Selection during industrialisation (1850--1950): air pollution killed lichens and darkened tree bark with soot. The dark form now had better camouflage against birds. The frequency of the carbonaria form increased dramatically in industrial areas (to > 95% in some populations).

Post-industrial reversal (1950--present): clean air legislation reduced pollution. Lichens recolonised trees, and the bark lightened. The light form regained its advantage, and the carbonaria form declined to < 10% in most areas.

Key points:

• The allele for dark colour is dominant ($C$ over $c$).
• The change in allele frequency was driven by differential predation (directional selection).
• This is one of the most well-documented examples of natural selection in action.
• Kettlewell (1955) demonstrated the selective advantage experimentally using mark-release-recapture, showing that dark moths had higher survival rates on polluted trees and light moths had higher survival rates on unpolluted trees.

17.2 Antibiotic Resistance

Mechanism of selection: when a patient takes an antibiotic, susceptible bacteria are killed, but any bacteria carrying resistance mutations survive and multiply. This is a classic example of directional selection.

Factors promoting resistance:

• Overuse of antibiotics (prescribing antibiotics for viral infections, which they cannot treat).
• Incomplete courses of antibiotics (patients stop taking antibiotics when they feel better, before all bacteria are killed).
• Use of antibiotics in agriculture (growth promoters in livestock, which selects for resistant bacteria).
• Poor infection control in hospitals (allowing resistant strains to spread).

MRSA (methicillin-resistant S. aureus): MRSA carries the mecA gene, which encodes a modified penicillin-binding protein (PBP2a) that has low affinity for methicillin and most other $\beta$-lactam antibiotics. MRSA is treated with vancomycin (a glycopeptide antibiotic that targets cell wall synthesis by a different mechanism).

17.3 Sickle Cell and Malaria: A Balanced Polymorphism

In regions where malaria is endemic, the heterozygous genotype ($Hb^A Hb^S$) has a selective advantage because it confers some resistance to malaria. However, the homozygous genotype ($Hb^S Hb^S$) causes sickle cell anaemia. The homozygous normal genotype ($Hb^A Hb^A$) is susceptible to malaria.

This is an example of heterozygote advantage (balancing selection), which maintains both alleles in the population at frequencies determined by the relative fitness of each genotype.

17.4 Artificial Selection (Selective Breeding)

Humans have been artificially selecting plants and animals for thousands of years:

Example	Trait Selected	Method
Dairy cattle	High milk yield	Breeding bulls and cows with the highest milk production records
Wheat	High yield, disease resistance, short stems (to prevent lodging)	Crossing different varieties; selecting offspring with desired traits
Dogs	Behaviour, appearance, size	Selective breeding over thousands of years, producing > 300 breeds
Disease-resistant crops	Resistance to fungal/bacterial/viral diseases	Screening plants for resistance; crossing with wild relatives that carry resistance genes

Artificial selection differs from natural selection in that humans (not the environment) determine which traits are advantageous. The process can be much faster than natural selection because selection is deliberate and intense.

18. Speciation: Mechanisms in Detail

18.1 Allopatric Speciation (Geographic Isolation)

Allopatric speciation occurs when populations are physically separated by a geographical barrier:

1. Geographic isolation: a physical barrier (mountain range, river, ocean, desert) divides a population into two or more subpopulations.
2. Reproductive isolation: the subpopulations cannot interbreed because they are physically separated.
3. Different selection pressures: each subpopulation experiences different environmental conditions, leading to different allele frequency changes through natural selection, genetic drift, and mutation.
4. Accumulation of genetic differences: over many generations, the subpopulations diverge genetically and phenotypically.
5. Reproductive isolation upon secondary contact: even if the geographic barrier is removed, the populations may no longer be able to interbreed (pre-zygotic or post-zygotic barriers have evolved).

Examples:

• The Kaibab and Abert's squirrels: separated by the Grand Canyon, they have diverged into distinct species.
• Darwin's finches: different islands in the Galapagos archipelago have different species of finch, each adapted to different food sources.

18.2 Sympatric Speciation

Sympatric speciation occurs without geographic isolation. It is more common in plants than animals.

Polyploidy in plants: errors in meiosis can produce gametes with a complete extra set of chromosomes (diploid gametes instead of haploid). When these fuse with normal haploid gametes, the offspring are triploid and sterile. When two diploid gametes fuse, the offspring are tetraploid (4n) and can self-fertilise or breed with other tetraploids, but not with the original diploid (2n) population. This creates instant reproductive isolation.

Example: modern wheat (Triticum aestivum) is a hexaploid (6n) that arose from hybridisation of three different diploid species.

18.3 Reproductive Isolating Mechanisms

Type	Mechanism	Example
Pre-zygotic (prevent mating or fertilisation)
Temporal isolation	Different breeding seasons or times of day	Two species of frog breed at different times of year
Habitat isolation	Different habitats within the same area	One species of insect breeds in water, another on land
Behavioural isolation	Different courtship displays or songs	Different bird species have different songs
Mechanical isolation	Incompatible reproductive structures	Different species of flower are pollinated by different insects with different mouthparts
Gametic isolation	Sperm and egg are incompatible	Marine species release gametes simultaneously but only same-species gametes fuse
Post-zygotic (prevent viable/fertile offspring)
Hybrid inviability	Zygote fails to develop properly	Sheep $\times$ goat hybrid dies during embryonic development
Hybrid sterility	Hybrid is sterile	Mule (horse $\times$ donkey): viable but sterile (cannot produce gametes due to odd chromosome number)
Hybrid breakdown	First-generation hybrid is fertile, but subsequent generations are not	Rice hybrids show reduced fertility in F2 generation

19. Molecular Evidence for Evolution

19.1 Comparative Genomics

Comparing DNA and protein sequences between species provides evidence for common ancestry and allows reconstruction of phylogenetic relationships:

• Cytochrome c: a highly conserved protein involved in the electron transport chain. The amino acid sequence of cytochrome c in humans differs from that in chimpanzees by 0 amino acids, from rhesus monkeys by 1, from dogs by 10, from yeast by 45. This pattern of differences is consistent with the known evolutionary relationships.
• DNA hybridisation: the degree of DNA-DNA hybridisation between two species reflects their genetic similarity. More closely related species have more complementary base sequences and form more stable hybrids.
• Molecular clocks: the rate of neutral mutations (mutations that do not affect fitness) is relatively constant over time. By counting the number of neutral differences between two species and dividing by the mutation rate, the time since they diverged from a common ancestor can be estimated.

19.2 Pseudogenes

Pseudogenes are non-functional copies of genes that have accumulated mutations rendering them non-functional. They provide evidence for evolution because:

1. The same pseudogenes are found in related species, in the same chromosomal locations (e.g., the GULO pseudogene for vitamin C synthesis is found in humans, chimpanzees, and gorillas, but is functional in most other mammals).
2. The pattern of shared mutations in pseudogenes is consistent with the known phylogenetic tree.

19.3 Endogenous Retroviruses (ERVs)

ERVs are viral DNA sequences that have been inserted into the genome of a germ cell and are inherited by subsequent generations. Shared ERVs at the same genomic loci in different species provide strong evidence for common ancestry, because the probability of independent insertion at the same location is vanishingly small.

20. Taxonomy: Classification Systems Compared

20.1 The Five Kingdom System (Whittaker, 1969)

Kingdom	Cell Type	Cell Wall	Nutrition	Examples
Prokaryotae (Monera)	Prokaryotic	Peptidoglycan	Autotrophic or heterotrophic	Bacteria, cyanobacteria
Protoctista	Eukaryotic	Some have cellulose	Autotrophic or heterotrophic	Amoeba, Paramecium, Chlorella
Fungi	Eukaryotic	Chitin	Heterotrophic (saprotrophic)	Mucor, Penicillium, yeast
Plantae	Eukaryotic	Cellulose	Autotrophic (photosynthetic)	Mosses, ferns, flowering plants
Animalia	Eukaryotic	None	Heterotrophic (ingestive)	Insects, fish, mammals

Problems with the five-kingdom system:

• Does not reflect evolutionary relationships (it is a phenetic system, based on shared characteristics, not phylogeny).
• Archaea are grouped with bacteria in Prokaryotae, but molecular evidence shows they are as different from bacteria as they are from eukaryotes.
• Some protists are more closely related to fungi, plants, or animals than to other protists.

20.2 The Three Domain System (Woese, 1990)

Based on ribosomal RNA (rRNA) gene sequencing:

Domain	Description	Key Features
Bacteria	Prokaryotic	Peptidoglycan cell wall; one circular chromosome; no introns; 70S ribosomes; ester-linked membrane lipids
Archaea	Prokaryotic	No peptidoglycan (pseudopeptidoglycan or protein S-layer); some have introns; 70S ribosomes; ether-linked membrane lipids; often extremophiles
Eukarya	Eukaryotic	Membrane-bound organelles; linear chromosomes; 80S ribosomes; ester-linked membrane lipids; introns common

20.3 Difficulties in Classification

1. Ring species: populations that can interbreed with neighbouring populations but not with populations at the other end of the ring (e.g., Larus gulls around the Arctic). Where do you draw the species boundary?
2. Horizontal gene transfer: bacteria and archaea can transfer genes between species by conjugation, transformation, and transduction, making phylogenetic trees more like networks.
3. Asexual organisms: the biological species concept (based on interbreeding) cannot be applied to organisms that reproduce asexually. Alternative concepts: morphological species concept, phylogenetic species concept.
4. Hybridisation: some plant species can hybridise and produce fertile offspring, blurring species boundaries.
5. Cryptic species: species that are morphologically identical but genetically distinct (e.g., Anopheles gambiae complex of malaria mosquitoes).

21. Conservation Biology: Strategies and Evaluation

21.1 In Situ Conservation

Conservation within the natural habitat:

Method	Description	Examples
National parks and nature reserves	Legally protected areas where human activities are restricted	Serengeti National Park (Tanzania); Yellowstone National Park (USA); Lake District National Park (UK)
Marine protected areas (MPAs)	Protected areas in oceans and coastal zones	Great Barrier Reef Marine Park (Australia)
Wildlife corridors	Strips of habitat connecting fragmented areas, allowing gene flow	Hedge rows in agricultural landscapes; overpasses for wildlife across roads
Community-based conservation	Local communities manage and benefit from conservation	CAMPFIRE programme in Zimbabwe (communities benefit from wildlife tourism)

Advantages of in situ conservation: preserves the entire ecosystem; allows natural evolutionary processes to continue; maintains ecological interactions; often more cost-effective than ex situ.

21.2 Ex Situ Conservation

Conservation outside the natural habitat:

Method	Description	Examples
Zoos and captive breeding	Breeding endangered species in captivity for later reintroduction	California condor recovery programme; Przewalski's horse
Botanic gardens	Growing and maintaining collections of endangered plants	Kew Gardens (UK); Millennium Seed Bank (stores seeds of > 40,000 species at -20 degrees C)
Seed banks	Long-term storage of seeds under controlled conditions	Svalbard Global Seed Vault (Norway) -- stores > 1 million seed samples
Cryopreservation	Freezing embryos, gametes, or tissues in liquid nitrogen (-196 degrees C)	Used for endangered animal species (e.g., coral sperm banks)
Tissue culture	Growing plants from small tissue samples in sterile conditions	Used for rare orchids and ferns

21.3 The CITES Convention

CITES (Convention on International Trade in Endangered Species) regulates international trade in wildlife:

Appendix	Species Covered	Trade Restrictions
I	Species threatened with extinction	Trade permitted only in exceptional circumstances (e.g., scientific research)
II	Species not threatened with extinction but may become so if trade is not controlled	Trade permitted with export permits
III	Species protected in at least one country	Trade permitted with export permits from that country

21.4 Measuring Conservation Success

Indicator	How Measured	Example
Population size	Census; mark-release-recapture	Population of mountain gorillas increased from ~250 (1980s) to ~1,000 (2020s)
Genetic diversity	Heterozygosity (proportion of gene loci that are heterozygous); number of alleles per locus	Florida panther: low heterozygosity ($H \approx 0.09$) due to bottleneck; improved by introducing Texas cougars
Habitat area	Remote sensing (satellite imagery); GIS	Rate of deforestation in the Amazon basin
Species richness	Quadrat sampling; transect surveys; camera traps	Number of species in a nature reserve before and after management intervention

22. Evolution: Evidence and Mechanisms

22.1 Types of Natural Selection

Type	Description	Effect on Population	When It Occurs
Directional selection	Favouring one extreme phenotype	Shift in the mean phenotype towards one extreme	Environment changes; new selective pressure
Stabilising selection	Favouring the intermediate phenotype; selecting against extremes	Reduction in variation; mean stays the same	Stable environment; intermediate is most fit
Disruptive selection	Favouring both extremes; selecting against the intermediate	Bimodal distribution; increase in variation	Environment favours two distinct niches; may lead to speciation

Examples:

• Directional: antibiotic resistance in bacteria (antibiotic selects for resistant individuals); peppered moth (industrial melanism during the Industrial Revolution).
• Stabilising: human birth weight (very low and very high birth weights have higher mortality); fur thickness in mammals in a stable climate.
• Disruptive: Lacertaspis lizards on islands (large lizards eat large insects; small lizards eat small insects; intermediate-sized lizards are outcompeted); Darwin's finches during drought (birds with either very large or very small beaks were favoured).

22.2 Evidence for Evolution

Type of Evidence	Examples
Fossil record	Sequence of fossils shows gradual change over time (e.g., horse evolution from Hyracotherium to Equus); transitional forms (e.g., Archaeopteryx -- feathered dinosaur with reptilian and avian features); relative dating (deeper layers contain older fossils)
Comparative anatomy	Homologous structures (same evolutionary origin, different function: pentadactyl limb in human, bat, whale, horse); analogous structures (different origin, similar function: insect wing and bird wing); vestigial structures (remnants of structures that had a function in ancestors: human appendix, pelvic bones in whales, hind limb buds in snakes)
Comparative embryology	Embryos of vertebrates are very similar in early development (e.g., pharyngeal pouches, tail, gill slits in fish, chicken, human embryos); suggests common ancestry
Molecular evidence	DNA and protein sequence comparisons; molecular clocks; shared pseudogenes; endogenous retroviruses (see Section 19)
Biogeography	Species on oceanic islands are similar to those on the nearest mainland (e.g., Darwin's finches resemble South American finches); the distribution of marsupials in Australia (separated from other continents early, allowing marsupials to diversify without competition from placental mammals)

22.3 Genetic Drift vs Natural Selection

Feature	Genetic Drift	Natural Selection
Mechanism	Random changes in allele frequency due to chance events	Non-random changes due to differential survival and reproduction
Direction	No predictable direction	Direction depends on which alleles confer fitness advantage
Strength	Stronger in small populations	Independent of population size (but operates on genetic variation, which is greater in large populations)
Effect on fitness	Can increase or decrease fitness (random)	Increases fitness (adaptive)
Feature	Genetic Drift	Natural Selection
-------	-------------	-----------------
Speed	Can cause rapid allele frequency changes in small populations	Generally slower (depends on selection coefficient)

23. Fieldwork Techniques and Data Analysis

23.1 Random Sampling with Quadrats

Procedure:

1. Lay out two tape measures at right angles along two edges of the study area.
2. Use random number tables (or a random number generator) to select coordinates.
3. Place a quadrat at each coordinate.
4. Count/estimate the abundance of each species within the quadrat.
5. Repeat for at least 10 quadrats (more for heterogeneous habitats).

Calculations from quadrat data:

Mean density per quadrat $= \frac◆LB◆\sum n_i◆RB◆◆LB◆k◆RB◆$ (where $n_i$ = number in quadrat $i$; $k$ = number of quadrats).

Total population estimate $= \text{mean density} \times \frac◆LB◆\text{total area}◆RB◆◆LB◆\text{quadrat area}◆RB◆$.

Standard deviation:

$s = \sqrt◆LB◆\frac◆LB◆\sum(x_i - \bar{x})^2◆RB◆◆LB◆n-1◆RB◆◆RB◆$

Standard error $= \frac◆LB◆s◆RB◆◆LB◆\sqrt{n}◆RB◆$.

95% confidence interval $= \bar{x} \pm 1.96 \times \text{standard error}$.

23.2 Belt Transect

A belt transect is used when studying changes in species distribution along an environmental gradient:

1. Lay a tape measure along the gradient (e.g., from high tide mark to low tide mark on a rocky shore).
2. Place quadrats at regular intervals along the tape (e.g., every 2 m).
3. Record species abundance in each quadrat.
4. Plot species abundance against distance along the transect.

23.3 Correlation and Association

Test	Data Type	Purpose	Null Hypothesis
Pearson's correlation coefficient ($r$)	Continuous data (both variables normally distributed)	Measures the strength and direction of a linear relationship between two variables	There is no correlation between the two variables ($r = 0$)
Spearman's rank correlation coefficient ($r_s$)	Ordinal data or non-normal continuous data	Measures the strength of a monotonic relationship	There is no correlation
Chi-squared ($\chi^2$) test	Categorical data (counts in categories)	Tests whether there is an association between two categorical variables	There is no association between the variables (observed = expected)

Chi-squared worked example:

Are plant species distributed independently of soil pH?

	Acidic soil	Neutral soil	Alkaline soil	Total
Species A	45	20	5	70
Species B	10	30	40	80
Total	55	50	45	150

Expected values: $E = \frac◆LB◆\text{row total} \times \text{column total}◆RB◆◆LB◆\text{grand total}◆RB◆$

$E_{A,\text{acidic}} = \frac◆LB◆70 \times 55◆RB◆◆LB◆150◆RB◆ = 25.7$

$\chi^2 = \sum \frac{(O - E)^2}{E} = \frac{(45-25.7)^2}{25.7} + \frac{(20-23.3)^2}{23.3} + \frac{(5-21)^2}{21} + \frac{(10-29.3)^2}{29.3} + \frac{(30-26.7)^2}{26.7} + \frac{(40-24)^2}{24}$

$\chi^2 = 14.5 + 0.47 + 12.2 + 12.7 + 0.41 + 10.7 = 50.98$

Degrees of freedom $= (\text{rows} - 1) \times (\text{columns} - 1) = 1 \times 2 = 2$.

Critical value at $p = 0.05$ with 2 df = 5.99. Since $50.98 > 5.99$, we reject the null hypothesis: there is a significant association between species distribution and soil pH.

24. The Hardy-Weinberg Principle: Extended Analysis

24.1 Derivation of the Hardy-Weinberg Equations

Consider a gene with two alleles, A and a, at frequencies $p$ and $q$ respectively.

If mating is random, the probability of each genotype in the next generation is:

Gamete from Father	Gamete from Mother	Offspring Genotype	Probability
A (probability $p$)	A (probability $p$)	AA	$p \times p = p^2$
A (probability $p$)	a (probability $q$)	Aa	$p \times q = pq$
a (probability $q$)	A (probability $p$)	Aa	$q \times p = pq$
a (probability $q$)	a (probability $q$)	aa	$q \times q = q^2$

Genotype frequencies: $p^2$ (AA) + $2pq$ (Aa) + $q^2$ (aa) = 1.

24.2 Conditions for Hardy-Weinberg Equilibrium

The Hardy-Weinberg principle assumes:

1. No mutations (no new alleles introduced).
2. Random mating (no sexual selection).
3. No gene flow (no migration into or out of the population).
4. Very large population size (no genetic drift).
5. No natural selection (all genotypes have equal fitness).

In reality, these conditions are rarely met completely, so most natural populations are not in Hardy-Weinberg equilibrium. The principle is useful as a null model: deviations from expected frequencies indicate that one or more of the assumptions is violated.

24.3 Using Hardy-Weinberg to Detect Selection

If the observed genotype frequencies differ significantly from the expected Hardy-Weinberg frequencies, this may indicate selection:

Example: In a population of snails, the observed and expected genotype frequencies are:

Genotype	Observed	Expected ($\mathrm{H\text{-}W}$)
BB (brown)	160	144 ($= 0.36 \times 400$)
Bb (brown)	120	192 ($= 0.48 \times 400$)
bb (yellow)	120	64 ($= 0.16 \times 400$)
Total	400	400

Allele frequencies: $p(\mathrm{B}) = \frac◆LB◆160 \times 2 + 120◆RB◆◆LB◆800◆RB◆ = 0.55$; $q(\mathrm{b}) = 0.45$.

The excess of bb homozygotes and deficiency of heterozygotes suggest negative assortative mating (like genotypes mate more often) or selection against heterozygotes (underdominance). A chi-squared test would determine whether the deviation is statistically significant.

25. Biodiversity Hotspots and Global Conservation Priorities

25.1 Biodiversity Hotspots

A biodiversity hotspot is a region that meets two criteria:

1. Contains at least 1,500 species of vascular plants as endemics (found nowhere else).
2. Has lost at least 70% of its original habitat.

Hotspot	Location	Key Features
Tropical Andes	South America	Highest plant diversity of any hotspot; many endemic amphibians and birds
Sundaland	Southeast Asia (Borneo, Sumatra, Java)	orangutans, tigers, Rafflesia; rapid deforestation
Madagascar	Indian Ocean	90% of wildlife found nowhere else; lemurs, baobabs
Mediterranean Basin	Southern Europe, North Africa, Middle East	25,000 plant species (50% endemic); heavily impacted by tourism, agriculture
Indo-Burma	India, Myanmar, Thailand, Vietnam	Tigers, elephants, gibbons; rapid habitat loss
Atlantic Forest (Brazil)	Eastern Brazil	20,000 plant species (8,000 endemic); only 12% of original forest remains

25.2 The Species-Area Relationship

The number of species in an area increases with the size of the area:

$S = cA^z$

Where $S$ = number of species; $A$ = area; $c$ and $z$ are constants ($z$ is typically 0.2--0.35 for islands).

Implication: if a habitat is reduced in size by 90%, the number of species will be reduced by approximately 50%. This is why habitat loss is the single greatest threat to biodiversity.

Example: if a forest of $100\ \mathrm{km^2}$ contains 500 species ($c = 100$, $z = 0.35$):

$S_1 = 100 \times 100^{0.35} = 100 \times 22.4 = 2240$

Wait, let me use the standard form. If a $1000\ \mathrm{km^2}$ area has 200 species:

$200 = c \times 1000^z$

If the area is reduced to $100\ \mathrm{km^2}$ (10% of original):

$S_2 = c \times 100^z = c \times (0.1 \times 1000)^z = c \times 0.1^z \times 1000^z = 0.1^z \times S_1$

With $z = 0.3$: $S_2 = 0.1^{0.3} \times 200 = 0.501 \times 200 = 100$ species lost (50%).

25.3 The Rio Convention (1992) and CBD Targets

The Convention on Biological Diversity (CBD), signed at the 1992 Earth Summit in Rio de Janeiro, has three main objectives:

1. Conservation of biological diversity.
2. Sustainable use of biological resources.
3. Fair and equitable sharing of benefits from genetic resources.

The Aichi Biodiversity Targets (2010--2020) included 20 targets (e.g., target 11: protect 17% of land and 10% of marine areas by 2020). Most targets were not met.

The post-2020 Global Biodiversity Framework (adopted at COP15 in 2022) includes the "30 by 30" target: protect 30% of land and ocean by 2030.

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tip

Diagnostic Test Ready to test your understanding of Biodiversity, Classification and Evolution? The diagnostic test contains the hardest questions within the A-Level specification for this topic, each with a full worked solution.

Unit tests probe edge cases and common misconceptions. Integration tests combine Biodiversity, Classification and Evolution with other biology topics to test synthesis under exam conditions.

See Diagnostic Guide for instructions on self-marking and building a personal test matrix.

26. Investigating Variation

26.1 Mean, Standard Deviation, and Standard Error

When analysing ecological data, it is essential to quantify variability:

Statistic	Formula	What It Measures
Mean ($\bar{x}$)	$\bar{x} = \frac◆LB◆\sum x_i◆RB◆◆LB◆n◆RB◆$	Central tendency
Standard deviation ($s$)	$s = \sqrt◆LB◆\frac◆LB◆\sum(x_i - \bar{x})^2◆RB◆◆LB◆n-1◆RB◆◆RB◆$	Spread of data around the mean
Standard error (SE)	$\mathrm{SE} = \frac◆LB◆s◆RB◆◆LB◆\sqrt{n}◆RB◆$	Precision of the mean estimate
95% CI	$\bar{x} \pm 1.96 \times \mathrm{SE}$	Range within which the true population mean is 95% likely to lie

26.2 Student's t-Test

Used to compare the means of two independent samples:

$t = \frac◆LB◆|\bar{x}_1 - \bar{x}_2|◆RB◆◆LB◆\sqrt◆LB◆\frac{s_1^2}{n_1} + \frac{s_2^2}{n_2}◆RB◆◆RB◆$

Degrees of freedom = $n_1 + n_2 - 2$.

Example: Soil pH is measured in two fields.

Field A: $\bar{x}_1 = 6.2$, $s_1 = 0.8$, $n_1 = 10$. Field B: $\bar{x}_2 = 5.1$, $s_2 = 0.7$, $n_2 = 10$.

$t = \frac◆LB◆|6.2 - 5.1|◆RB◆◆LB◆\sqrt◆LB◆\frac{0.64}{10} + \frac{0.49}{10}◆RB◆◆RB◆ = \frac◆LB◆1.1◆RB◆◆LB◆\sqrt{0.113}◆RB◆ = \frac{1.1}{0.336} = 3.27$

Degrees of freedom $= 18$. Critical value at $p = 0.05$ with 18 df $= 2.101$.

Since $3.27 > 2.101$, we reject the null hypothesis: there is a statistically significant difference in soil pH between the two fields.

27. Evidence for Evolution

27.1 Types of Evidence

Type of Evidence	Examples	What It Shows
Fossil record	Transitional fossils (e.g., Archaeopteryx -- between reptiles and birds; Tiktaalik -- between fish and tetrapods; Ambulocetus -- between land mammals and whales)	Shows gradual change over time; reveals the sequence of evolution
Comparative anatomy	Homologous structures (pentadactyl limb: human arm, bat wing, whale flipper, cat leg -- same bone arrangement, different functions); analogous structures (insect wing vs bird wing -- different origin, similar function)	Homologous = common ancestry; Analogous = convergent evolution
Comparative biochemistry	Universal genetic code; cytochrome c amino acid sequence (more similar in closely related species); DNA-DNA hybridisation	Molecular evidence for common ancestry
Comparative embryology	Early vertebrate embryos all look similar (pharyngeal pouches, tail, somites); suggest common ancestry	Developmental similarities reflect evolutionary relationships
Biogeography	Species on oceanic islands resemble those on nearest mainland (e.g., Galapagos finches resemble South American finches); continental drift explains distribution of fossils (e.g., Mesosaurus in South America and Africa)	Geographic patterns consistent with evolution, not independent creation
Direct observation	Antibiotic resistance in bacteria; pesticide resistance in insects; Darwin's finches (beak size changes with food availability)	Evolution can be observed in real time

27.2 Molecular Clock

The molecular clock uses the rate of neutral mutations to estimate when two species diverged from a common ancestor:

$\text{Time since divergence} = \frac◆LB◆\text{Number of nucleotide differences}◆RB◆◆LB◆2 \times \text{Mutation rate per year}◆RB◆$

Assumptions:

• The mutation rate is constant over time.
• Most mutations are neutral (not affected by natural selection).
• The rate is the same in both lineages.

Example	Species Compared	Cytochrome c Amino Acid Differences	Estimated Divergence
Human vs chimpanzee	0 differences	~6 million years ago
Human vs rhesus monkey	1 difference	~25 million years ago
Human vs dog	10 differences	~80 million years ago
Human vs yeast	45 differences	~1.5 billion years ago

28. Classification Systems

28.1 The Three-Domain System (Woese, 1990)

Domain	Cell Type	Cell Wall	Membrane Lipids	Genetic Material	Examples
Bacteria	Prokaryotic	Peptidoglycan	Ester-linked (straight chain fatty acids)	Single circular chromosome; no histones	E. coli, Staphylococcus, Cyanobacteria
Archaea	Prokaryotic	Pseudopeptidoglycan (some); or no cell wall	Ether-linked (isoprene chains)	Single circular chromosome; histone-like proteins	Methanogens, Halophiles, Thermophiles
Eukarya	Eukaryotic	Cellulose (plants), chitin (fungi), none (animals)	Ester-linked	Linear chromosomes in nucleus; histones	Animals, plants, fungi, protists

28.2 The Five-Kingdom System

Kingdom	Cell Type	Nutrition	Cell Wall	Examples
Animalia	Eukaryotic	Heterotrophic (ingestion)	None	Mammals, insects, fish, birds
Plantae	Eukaryotic	Autotrophic (photosynthesis)	Cellulose	Flowering plants, conifers, ferns, mosses
Fungi	Eukaryotic	Heterotrophic (absorption; extracellular digestion)	Chitin	Mushrooms, yeasts, moulds
Protoctista (Protista)	Eukaryotic	Mixed (autotrophic and heterotrophic)	Some have cellulose	Amoeba, Paramecium, Chlorella, Plasmodium
Prokaryotae (Monera)	Prokaryotic	Mixed	Peptidoglycan (bacteria)	Bacteria (now split into Domains Bacteria and Archaea)

28.3 Phylogenetic Classification vs Traditional Classification

Feature	Phylogenetic (Cladistics)	Traditional (Phenetics)
Basis for grouping	Evolutionary relationships (shared ancestry)	Overall similarity (morphology, anatomy, physiology)
Key tool	DNA and protein sequencing; cladograms	Observable characteristics; dichotomous keys
Groupings	Monophyletic groups only (ancestor + ALL descendants)	May include paraphyletic or polyphyletic groups
Example	Birds are grouped WITHIN reptiles (share common ancestor with crocodiles)	Birds are a separate class from reptiles
Advantages	Reflects true evolutionary history; predictive power	Simple; uses observable features; practical for field identification

29. Biodiversity Hotspots and Conservation

29.1 Biodiversity Hotspots

A biodiversity hotspot is a region with:

1. High species richness (at least 1,500 endemic plant species -- species found nowhere else).
2. High threat level (has lost at least 70% of its original primary vegetation).

Hotspot	Location	Key Features
Tropical Andes	South America	Highest plant diversity on Earth; many endemic species (e.g., spectacled bear, Andean condor)
Sundaland	Southeast Asia (Borneo, Sumatra, Java)	Orangutan, tiger, Rafflesia; rapid deforestation
Madagascar	Indian Ocean	90% of wildlife is endemic; lemurs, baobab trees
Mediterranean Basin	Southern Europe, North Africa, Middle East	25,000 plant species (50% endemic); suffers from habitat fragmentation and tourism
Indo-Burma	Southeast Asia	Freshwater turtle diversity; rapid habitat loss
Atlantic Forest (Brazil)	Eastern Brazil	20,000 plant species (8,000 endemic); only 12% of original forest remains
Cape Floristic Region	South Africa	9,600 plant species (70% endemic); fynbos vegetation; proteas, heathers

29.2 Conservation Strategies

Strategy	Description	Example
In situ conservation	Protecting species in their natural habitat	National parks (e.g., Serengeti, Yellowstone); nature reserves; SSSIs (Sites of Special Scientific Interest); marine protected areas
Ex situ conservation	Protecting species outside their natural habitat	Zoos; botanical gardens; seed banks (e.g., Millennium Seed Bank, Kew); cryopreservation of genetic material
Captive breeding	Breeding endangered species in captivity for later reintroduction	California condor; Przewalski's horse; golden lion tamarin
Habitat corridors	Connecting fragmented habitats to allow gene flow and migration	Wildlife bridges; hedgerow networks; riparian corridors along rivers
CITES	Convention on International Trade in Endangered Species of Wild Fauna and Flora; regulates international trade in endangered species	Bans trade in ivory, rhino horn, tiger parts

30. Fieldwork Techniques

30.1 Random Sampling

Technique	Description	How to Ensure Randomness
Quadrat sampling	A square frame (typically 0.5 m $\times$ 0.5 m or 1 m $\times$ 1 m) is placed randomly in the study area; organisms within the quadrat are counted	Use a random number generator to select coordinates; throw the quadrat over your shoulder without looking
Transect sampling	A line (tape measure) is laid across the habitat; quadrats are placed at regular intervals along the line	Useful for studying changes in species distribution across an environmental gradient (e.g., from sea shore inland)
Sweep netting	A net is swept through vegetation to catch mobile invertebrates	Standardise number of sweeps; compare between sites
Pitfall trapping	Containers sunk into the ground; ground-dwelling invertebrates fall in	Position randomly; check regularly; add preservative
Kick sampling	Riverbed is disturbed by kicking; invertebrates are carried into a net downstream	Standardise kick time and area; used for freshwater invertebrate surveys

30.2 Estimating Population Size

Method	Formula	When to Use
Quadrat density	$\text{Population} = \text{mean density per quadrat} \times \text{total area}$	Plants and sessile (non-moving) animals
Mark-release-recapture (Lincoln index)	$N = \frac◆LB◆M \times C◆RB◆◆LB◆R◆RB◆$ (M = marked first catch, C = total second catch, R = recaptured marked)	Mobile animals
Belt transect	Count organisms in quadrats along a continuous transect	Studying distribution along a gradient

Assumptions of mark-release-recapture:

1. Marked individuals mix completely with the population.
2. The proportion of marked to unmarked individuals in the second sample is the same as in the whole population.
3. No marks are lost.
4. Marks do not affect survival or behaviour.
5. Population is closed (no births, deaths, immigration, or emigration between samples).

31. Speciation

31.1 Allopatric Speciation (Geographic Isolation)

Step	What Happens
1	A population is physically separated by a geographic barrier (mountain range, river, ocean, desert)
2	Gene flow between the two populations stops (no interbreeding)
3	Different selection pressures act on each population (different environments, food sources, predators, climate)
4	Natural selection favours different alleles in each population
5	Mutations arise independently in each population
6	Over many generations, the populations become so genetically different that they can no longer interbreed to produce fertile offspring (reproductive isolation)
7	They are now separate species

31.2 Reproductive Isolation Mechanisms

Type	Mechanism	Example
Prezygotic (prevent mating or fertilisation)
Temporal isolation	Different breeding seasons	Two species of frog that breed at different times of year
Habitat isolation	Different habitats within the same area	One species of insect lives in oak trees; another in pine trees
Behavioural isolation	Different courtship behaviours or songs	Different bird species have different songs; fireflies have different flash patterns
Mechanical isolation	Incompatible reproductive structures	Different shapes of genitalia in insect species
Gametic isolation	Gametes cannot fuse (sperm cannot fertilise egg)	Sea urchins release gametes simultaneously but species-specific proteins prevent cross-fertilisation
Postzygotic (prevent viable/fertile offspring)
Hybrid inviability	Zygote forms but does not develop properly	Frog species hybrid dies at the embryo stage
Hybrid sterility	Hybrid is viable but sterile (cannot reproduce)	Mule (horse $\times$ donkey); liger (lion $\times$ tiger)
Hybrid breakdown	First-generation hybrid is viable and fertile, but subsequent generations are not	Some plant hybrids

32. Natural Selection in Detail

32.1 Types of Selection

Type	Description	Effect on Population	Example
Stabilising selection	Favouring the average (intermediate phenotype); selecting against extremes	Reduces variation; narrows the range; mean stays the same	Human birth weight (very low and very high birth weights have higher mortality; average weight is favoured)
Directional selection	Favouring one extreme phenotype; selection shifts the mean in one direction	Changes the mean of the population	Antibiotic resistance (bacteria with resistance genes survive and reproduce; mean shifts towards resistance); Peppered moth (industrial melanism)
Disruptive selection	Favouring both extremes; selecting against the intermediate	Increases variation; may lead to speciation	Beak size in Darwin's finches (during drought, large and small beaks are favoured; intermediate beaks are disadvantageous)

32.2 Conditions for Natural Selection

Condition	Description
Variation	Individuals in a population must differ in their characteristics (genetic variation)
Heritability	The variation must be genetic (inherited from parents); acquired characteristics are NOT passed on
Differential survival and reproduction	Some variants are more likely to survive and reproduce than others (selection pressure)
Overproduction of offspring	More offspring are produced than can survive (competition for resources)

33. The Peppered Moth: A Case Study

33.1 Background

Feature	Details
Species	Biston betularia (peppered moth)
Two forms (morphs)	Light (typica) and dark (carbonaria)
Cause of polymorphism	Single gene mutation (dominant carbonaria allele)
Habitat	Trees with lichen-covered bark (light) and soot-blackened bark (industrial areas)

33.2 The Story

Period	Conditions	Selective Pressure	Outcome
Pre-industrial England (before 1850)	Trees covered with light-coloured lichen	Light moths were better camouflaged; dark moths were easily seen and eaten by birds	Light morph was common (~98%); dark morph was rare (~2%)
Industrial Revolution (1850--1950)	Air pollution killed lichen; tree bark became dark with soot	Dark moths were now better camouflaged; light moths were easily seen	Dark morph increased to ~95% in industrial areas; directional selection
Post-industrial (1950--present)	Clean air laws reduced pollution; lichen regrew on trees	Light moths were once again better camouflaged; dark moths became more visible	Light morph has increased again in clean areas; reverse directional selection

33.3 What This Demonstrates

Principle	Evidence from the Peppered Moth
Natural selection causes evolution	The frequency of the carbonaria allele changed in response to environmental change
Selection pressure can change	Pollution altered the selective environment (bird predation)
Evolution is reversible	When the environment changed back, the allele frequencies shifted again
Genetic variation is the raw material	The mutation for dark colour existed at low frequency before industrialisation; it became advantageous when conditions changed

34. Cladistics

34.1 Building a Cladogram

Step	Description
1	Select a group of species to study
2	Identify shared derived characteristics (synapomorphies) -- traits that are shared because of common ancestry (not convergent evolution)
3	Determine which species share the most characteristics (these are most closely related)
4	Construct a branching diagram (cladogram) showing the evolutionary relationships
5	Include an outgroup (a species known to be outside the group being studied) to root the cladogram

34.2 Reading a Cladogram

Feature	What It Shows
Branch point (node)	Represents a common ancestor of all species above that point
Branch length	In some cladograms, longer branches = more genetic change; in others, branch lengths are not meaningful
Species closest together on the cladogram	Share a more recent common ancestor; are more closely related
Number of shared derived characteristics	Species that share more derived characteristics are more closely related

35. Antibiotic Resistance: An Evolutionary Perspective

35.1 How Antibiotic Resistance Arises

Step	What Happens
1	A random mutation occurs in a bacterial chromosome or a resistance gene is acquired via a plasmid (horizontal gene transfer)
2	The mutation/gene confers resistance to an antibiotic (e.g., by producing an enzyme that inactivates the drug, altering the drug's target, or pumping the drug out of the cell)
3	When the antibiotic is present, susceptible bacteria are killed; resistant bacteria survive and reproduce
4	The resistance allele frequency increases in the population (directional selection)
5	Resistant bacteria spread to other patients, hospitals, and communities

35.2 Mechanisms of Antibiotic Resistance

Mechanism	Example
Enzymatic inactivation	$\beta$-lactamase enzymes break down $\beta$-lactam antibiotics (penicillin, amoxicillin)
Target modification	MRSA (methicillin-resistant S. aureus) has altered penicillin-binding protein (PBP2a) that does not bind methicillin
Efflux pumps	Bacterial pumps actively export antibiotics out of the cell (e.g., tetracycline efflux pumps)
Reduced permeability	Mutations that reduce porin size in Gram-negative bacteria, preventing antibiotic entry
Alternative pathway	Bacteria develop a metabolic pathway that bypasses the drug's target

35.3 Strategies to Reduce Antibiotic Resistance

Strategy	Description
Complete the course	Patients must finish their prescribed antibiotic course (even if they feel better); prevents partially-resistant bacteria from surviving
Reduce unnecessary prescriptions	Only prescribe antibiotics for bacterial infections (not viral infections like colds and flu)
Infection control	Hand hygiene in hospitals; isolation of patients with resistant infections; disinfection of surfaces
Research and development	Develop new antibiotics; find new antimicrobial compounds; explore bacteriophage therapy
Public education	Awareness campaigns about the dangers of antibiotic misuse
Agricultural restrictions	Ban or restrict the use of antibiotics as growth promoters in livestock (already implemented in the EU)

36. Using Dichotomous Keys

36.1 What Is a Dichotomous Key?

A dichotomous key is a tool used to identify organisms based on a series of paired statements (couplets). Each statement leads to another couplet until the organism is identified.

36.2 Rules for Constructing a Dichotomous Key

Rule	Description
Use paired statements	Each couplet has two mutually exclusive options (e.g., "1a. Wings present" vs "1b. Wings absent")
Use observable characteristics	Base the key on features that can be easily observed (morphological, anatomical)
Be specific	Avoid vague terms (e.g., "large" vs "small"); use measurable features where possible
Each step leads to one outcome	Each statement should lead either to the next couplet or to the identification of the organism
Avoid overlapping categories	The two options in each couplet must not overlap (no organism should fit both)
Test the key	Verify that the key works correctly by testing it against known specimens

36.3 Example: Dichotomous Key for Common UK Trees

1a. Leaves are needles (conifer) ............. Go to 4
1b. Leaves are broad (deciduous) ........... Go to 2

2a. Leaves have lobed edges ............... Go to 3
2b. Leaves have smooth edges .............. Go to 5

3a. Leaves have 3--5 pointed lobes ......... Oak (_Quercus_)
3b. Leaves have 5 deep lobes, rounded at the tips .... Sycamore (_Acer pseudoplatanus_)

4a. Needles in bundles of 2 .............. Scots pine (_Pinus sylvestris_)
4b. Needles in bundles of 5 .............. European larch (_Larix decidua_)

5a. Leaves are heart-shaped ............. Lime (_Tilia_)
5b. Leaves are oval with a pointed tip ... Beech (_Fagus sylvatica_)

37. Taxonomic Hierarchy

37.1 The Hierarchical Classification System

Rank	Example (Human)	Example (Dog)	Example (Oak Tree)
Domain	Eukarya	Eukarya	Eukarya
Kingdom	Animalia	Animalia	Plantae
Phylum	Chordata	Chordata	Spermatophyta
Class	Mammalia	Mammalia	Eudicots
Order	Primates	Carnivora	Fagales
Family	Hominidae	Canidae	Fagaceae
Genus	Homo	Canis	Quercus
Species	Homo sapiens	Canis lupus familiaris	Quercus robur

37.2 Three-Domain vs Five-Kingdom System

Feature	Three-Domain System (Woese)	Five-Kingdom System
Proposed by	Carl Woese (1990)	Robert Whittaker (1969)
Basis	Molecular (rRNA sequencing)	Morphological (observable characteristics)
Top-level groups	Bacteria, Archaea, Eukarya	Animalia, Plantae, Fungi, Protoctista, Prokaryotae
Archaea are	Separate domain from Bacteria	Grouped with Bacteria in Prokaryotae

38. Evidence for Evolution: Molecular Evidence

38.1 Comparing DNA Sequences

Principle	Description
DNA hybridisation	DNA from two species is unwound, mixed, and allowed to reanneal; the more similar the sequences, the more hydrogen bonds form, the higher the melting temperature
Percentage sequence similarity	Compare the base sequences of a specific gene across species; the greater the similarity, the more closely related the species
Cytochrome c	A highly conserved protein found in all aerobic organisms; comparing its amino acid sequence reveals evolutionary relationships
Haemoglobin	Comparing alpha- and beta-globin gene sequences across species shows patterns of divergence that match the fossil record

38.2 The Molecular Clock

Feature	Description
Principle	Neutral mutations accumulate in DNA at a roughly constant rate over time
Use	By counting the number of neutral mutations that differ between two species, you can estimate the time since they diverged from a common ancestor
Calibration	The clock must be calibrated using the fossil record (known divergence times from fossils)
Limitations	Mutation rate is not perfectly constant (varies between genes, between lineages, and over time); natural selection can distort the clock; generation time affects the number of mutations per year

39. Types of Natural Selection

39.1 Directional Selection

Feature	Description
What happens	Favours individuals at one extreme of the phenotypic range; the mean phenotype shifts in one direction
Example	Antibiotic resistance: bacteria with resistance genes survive antibiotic treatment; non-resistant bacteria die; the mean resistance of the population increases
When it occurs	When the environment changes; a new selective pressure favours one extreme
Graph effect	The frequency distribution curve shifts to one side

39.2 Stabilising Selection

Feature	Description
What happens	Favours individuals with the intermediate phenotype; extremes are selected against
Example	Human birth weight: very low birth weight babies have reduced survival; very high birth weight babies cause complications during birth; intermediate birth weight is favoured
When it occurs	In stable environments where the current mean is optimal
Graph effect	The frequency distribution curve becomes narrower and taller

39.3 Disruptive Selection

Feature	Description
What happens	Favours individuals at both extremes; intermediate phenotypes are selected against
Example	Darwin's finches: during drought, only large and small seeds were available (medium seeds became scarce); birds with large beaks (large seeds) and small beaks (small seeds) were favoured; medium-beaked birds were selected against
When it occurs	When the environment favours two distinct phenotypes
Graph effect	The frequency distribution curve develops two peaks (bimodal); can lead to speciation over time

40. Speciation

40.1 Allopatric Speciation (Geographic Isolation)

Step	Description
1. Geographic separation	A physical barrier (mountain range, river, ocean) divides a population into two groups
2. No gene flow	The two populations cannot interbreed; alleles cannot be shared between them
3. Different selection pressures	Each population experiences different environmental conditions and different mutations arise independently
4. Allele frequencies change	Natural selection, genetic drift, and mutation cause the allele frequencies of each population to diverge over many generations
5. Reproductive isolation	Eventually, the two populations become so different that even if the geographic barrier is removed, they cannot interbreed to produce fertile offspring -- they are now separate species

40.2 Sympatric Speciation (Without Geographic Isolation)

Feature	Description
What it is	Speciation that occurs within the same geographic area
Mechanism	Usually involves polyploidy (especially in plants): a mutation causes an individual to have extra sets of chromosomes (e.g., tetraploid, 4n); the polyploid individual can only reproduce with other polyploids; this creates instant reproductive isolation
Example	Modern wheat (Triticum aestivum) is a hexaploid (6n) that arose from hybridisation of three different species

40.3 Reproductive Isolation Mechanisms

Type	Example
Seasonal isolation	Different breeding seasons (e.g., two species of frog breed at different times of year)
Behavioural isolation	Different courtship displays or mating calls (e.g., different bird songs)
Mechanical isolation	Physical incompatibility of reproductive structures (e.g., lock-and-key fit of insect genitalia)
Gametic isolation	Sperm cannot fertilise the egg of a different species (e.g., sea urchin gametes recognise species-specific proteins on the egg surface)
Hybrid inviability	Hybrid offspring are produced but do not survive to reproductive age
Hybrid sterility	Hybrid offspring are healthy but sterile (e.g., mule = horse $\times$ donkey; mules are sterile)

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