5.2.1 Genetic variation within a population

Variation within populations

1. Individuals of the same species share many features, but a population usually contains a wide range of inherited differences.
2. Members of a population usually have the same kinds of genes, while the alleles they carry and the combinations of those alleles can differ.
3. A gene can have several alleles across a population, even though a diploid individual normally carries only two copies of that gene, one inherited from each parent.
4. Genetic variation therefore includes both differences between DNA base sequences and differences in the combinations of alleles present in individuals.
5. Two organisms can look very similar while differing at many positions in their DNA, so visible appearance alone underestimates genetic variation.
6. The illustration shows different bases at the same position in a DNA sequence, which is one possible form of genetic variation.

Sources of genetic differences

1. Mutations are the original source of new genetic variants, including new alleles.
2. They occur without being directed towards a particular useful outcome, so an organism does not produce a specific mutation because it needs that characteristic.
3. A mutation can be passed to offspring only if the altered genetic material is included in the cells that produce the offspring.
4. In sexually reproducing animals, a mutation confined to an ordinary body cell is generally not passed to the next generation.
5. Sexual reproduction brings existing alleles together in new combinations, which explains why offspring usually differ from both their parents and their siblings.
6. Meiosis produces genetically different gametes, and the random meeting of gametes during fertilisation adds further combinations.
7. The chromosome combinations in the diagram illustrate this mixing of inherited material; the mixing rearranges existing alleles rather than creating new versions of them.

Genetic and visible variation

1. Genotype is the combination of alleles an organism has.
2. Phenotype is the observable characteristics of an organism, produced by its genotype and its interactions with the environment.
3. A difference in phenotype can result from genetic differences, environmental differences or both, so visible variation is not automatically evidence of different alleles.
4. For example, a plant may be short because it carries alleles associated with short growth, because it receives too few mineral ions, or because both factors affect it.
5. Most genetic variants do not change the phenotype, while some alter a characteristic and a small number can have a large effect.
6. A variant with no obvious effect is still a DNA difference and therefore still contributes to genetic variation.
7. When comparing individuals, use evidence about their inherited material to distinguish genetic variation from changes caused only by their surroundings.

5.2.2 Developments in classification systems

Grouping organisms

1. A classification system organises the variety of living organisms so that their features can be compared and information about them can be shared.
2. Classifications can use external appearance, internal structure, cell organisation and molecular information.
3. The traditional hierarchy contains kingdom, phylum, class, order, family, genus and species, with domain placed above kingdom in a domain-based system.
4. Each smaller group lies within a larger group, so species in the same genus also share a family.
5. A natural classification aims to place more closely related organisms together in the smaller groups.

Artificial and natural systems

1. An artificial system may use a few easily observed features, such as where organisms live or whether they have wings, because these make sorting convenient.
2. Grouping all swimming animals together would combine fish with mammals such as dolphins, even though those animals do not share a recent common ancestor.
3. A natural system uses evidence from many characteristics to represent common ancestry, rather than relying only on a convenient resemblance.
4. Shared internal structures can reveal relationships that a similar outward shape hides, so both the number and biological significance of shared features matter.
5. A shark, penguin and dolphin all have structures that help them swim, but similarity in function alone does not establish a close evolutionary relationship.
6. The penguin and dolphin have corresponding forelimb bones inherited from a shared vertebrate ancestor, while their streamlined swimming forms do not place either within the fish.

DNA reveals relationships

1. Phylogeny is the evolutionary history and relationships of organisms.
2. DNA sequencing determines the order of bases in DNA, allowing scientists to compare corresponding sequences from different organisms.
3. For comparable DNA regions, a greater similarity in base sequence generally indicates a closer evolutionary relationship and a more recent common ancestor.
4. Differences build up as lineages diverge, so comparing many corresponding sequences provides stronger evidence than comparing one short fragment.
5. Scientists can also compare amino acid sequences in proteins and combine molecular findings with structural evidence.
6. Molecular comparisons provide evidence about organisms that look very different as well as organisms whose appearance is misleadingly similar.
7. If this evidence conflicts with an existing grouping, scientists can revise the classification to reflect the better-supported relationships.
8. Improved microscopy also revealed differences in cell structures, helping scientists distinguish groups that earlier methods could not separate.

Reading evolutionary trees

1. A phylogenetic tree is a branching diagram representing a proposed pattern of evolutionary relationships.
2. A branch point represents a common ancestor, and the descendants connected through that point share that ancestor.
3. To compare two species, trace their branches backwards to the first common branch point, then compare this with the branch points shared with other species.
4. Species whose branches meet at a more recent common ancestor are more closely related, regardless of how close their names appear on the page.
5. A labelled characteristic on a branch indicates a feature shared by descendants of that branch in the simplified tree.
6. Evidence can change the groups shown on a tree, as illustrated by the grouping of birds with other descendants within the reptile lineage.
7. The three-domain system separates Bacteria, Archaea and Eukaryota, reflecting molecular and cellular differences that older classifications did not fully recognise.
8. Bacteria and archaea both lack a membrane-bound nucleus, but molecular differences support their placement in distinct domains.
9. Eukaryota includes organisms whose cells contain nuclei, including animals, plants, fungi and protists.
10. The broad ancestry diagram shows how present-day groups can be traced back towards shared ancestors; the branching relationships are the feature to interpret here.
11. Some trees include a time scale, but branch length indicates time only when the diagram explicitly provides that information.
12. The DNA comparison diagram illustrates how molecular differences can inform estimates of divergence, although exact dates cannot be read from an unscaled tree.

Names and identification

1. A binomial name is the two-part scientific name of a species, consisting of its genus name and specific name.
2. The genus starts with a capital letter and the specific name uses a lower-case initial, with both words italicised in print or underlined separately by hand.
3. For example, the tiger belongs to the genus Panthera and has the specific name tigris, as the naming illustration shows.
4. Scientific names allow people using different languages to identify the same species, avoiding ambiguity caused by shared common names.
5. An identification key guides the identification of a specimen using observable features, whereas a natural classification describes how organisms are related.
6. The leaf key illustrates a sequence of paired choices, but the order of those choices does not itself represent evolutionary ancestry.

5.2.3 How evolution occurs through natural selection

Selection favours inherited variants

1. Individuals within a population have different alleles, and some of these genetic differences produce different phenotypes.
2. Mutations are the original source of the variants on which natural selection acts, but they do not occur in response to an organism needing a particular advantage.
3. A selection pressure, such as predation, disease or shortage of food, affects the reproductive success of individuals with different characteristics.
4. A phenotype is advantageous only in relation to the conditions in which the organism lives, so a characteristic that helps in one environment may be less useful in another.
5. Organisms often produce more offspring than the available resources can support, which creates competition for resources such as food, light, space and water.
6. Individuals with a favourable inherited phenotype are more likely to survive long enough to reproduce successfully.
7. Their offspring may inherit the alleles responsible for that phenotype, so those alleles are represented more frequently in the next generation.
8. When this difference in reproductive success continues across generations, the advantageous alleles and associated phenotypes usually become more common.
9. The result depends on inheritance as well as survival, because surviving without producing offspring does not pass an allele to the next generation.

Camouflage and predation

1. In the illustrated mouse population, fur colour varies and the background is dark.
2. Dark fur provides better camouflage, making dark mice less conspicuous to visual predators than pale mice.

Changing selection pressures

1. Reproductive success means the contribution an organism makes to future generations through its offspring.
2. Biological fitness concerns reproductive success in a particular environment, so it does not simply mean being the strongest or largest organism.
3. If the surroundings change from dark rock to pale sand, pale fur may become advantageous because the relationship between colour and visibility has changed.
4. A change in conditions can therefore favour a different phenotype without directing a useful mutation to occur.
5. A trait may also involve a trade-off, helping with one pressure while making another activity more difficult.
6. A full explanation identifies the relevant pressure and weighs the effect of the characteristic in that specific setting.

5.2.4 Evolution as change over time

Populations change across generations

1. Evolution concerns changes in inherited characteristics across successive generations, so the population is the unit whose characteristics are compared over time.
2. A population can evolve when the relative abundance of inherited variants changes, even if it still belongs to the same species.
3. Natural selection can produce this change when individuals carrying particular inherited variants contribute more offspring to later generations.
4. This links present-day populations to earlier populations through descent with modification, meaning inheritance accompanied by changes across generations.
5. Growth, learning and changes caused only by the environment during one individual's life do not by themselves show evolution.
6. For example, a person developing larger muscles through training is a change within an individual, without evidence that the population's inherited characteristics have changed.
7. An increase in the total number of organisms is also insufficient evidence, because the relative proportions of inherited characteristics might remain the same.

New species can form

1. The fertile-offspring definition of species is useful for sexually reproducing organisms, although it cannot be applied directly to organisms that reproduce only asexually.
2. Evolution may lead to speciation, but a change in one inherited characteristic does not automatically create a new species.
3. One route begins when populations become isolated, for example when a geographical barrier prevents individuals from interbreeding.
4. Separate populations then stop exchanging alleles through reproduction, allowing inherited differences to accumulate independently.
5. Different conditions can favour different characteristics in each population, while new mutations can also introduce differences.
6. Over many generations, the populations may become so different that individuals can no longer interbreed successfully to produce fertile offspring.
7. They are then reproductively isolated, which marks the formation of distinct species under the fertile-offspring definition.
8. Geographical separation alone does not show that speciation has occurred, because separated populations may still be capable of producing fertile offspring together.

Branching ancestry and timescales

1. A common ancestor is an ancestral organism or population from which two or more later lineages descend.
2. When one ancestral lineage gives rise to separate descendant lineages, evolution forms a branching pattern rather than a single ladder from simple to advanced organisms.
3. Present-day species at different tips of a tree may share an earlier ancestor without one present-day species having evolved directly from the other.
4. The branching diagram represents inherited differences accumulating in descendant lineages, with branch points indicating shared ancestors.
5. Evolution has no predetermined goal, and natural selection favours characteristics according to the conditions encountered by each population.
6. Major differences between lineages can accumulate over very long periods, but evolutionary change does not always require millions of years.
7. The speed at which a measurable change appears depends on factors such as generation time, available genetic variation and the strength of selection pressures.
8. Organisms with short generation times can pass through many generations during a short period, allowing inherited changes to be detected sooner.

5.2.5 Evidence for evolution

Fossils preserve evidence

1. The fossil record is the collection of fossils and information about where and when the organisms they represent lived.
2. Fossils can preserve body parts, such as bones, teeth and shells, or traces, such as footprints, burrows and impressions.
3. Rapid burial by sediment can protect remains from scavengers and reduce disturbance, increasing the chance that a record of the organism survives.
4. Hard structures may remain while softer tissues decay, and minerals can replace or fill parts of the remains as the surrounding sediment becomes rock.
5. An organism may also leave a mould or impression that records its shape after the original material has disappeared.
6. Some remains are preserved when conditions greatly reduce decay, including freezing or entrapment in resin that later forms amber.
7. A fossil does not have to be a complete organism, and its biological value depends on which features or activities have been preserved.

The record shows change

1. Comparing fossils from rocks of different ages reveals that the kinds of organisms living on Earth have changed.
2. In a sequence of sedimentary layers that has not been overturned or heavily disturbed, lower layers are generally older than the layers above them.
3. The ages of the rocks therefore provide a sequence in which fossil characteristics can be compared.
4. Some extinct organisms share features with later organisms, supporting the idea that later lineages descended from earlier forms.
5. Fossils with combinations of features associated with different groups can provide evidence for evolutionary relationships and changes in body structure.
6. A conclusion about change is stronger when it identifies the actual feature, describes how that feature differs between fossils, and relates the difference to their ages.

Gaps in the fossil record

1. Fossilisation is uncommon because most organisms are eaten, decomposed or physically broken apart before preservation can occur.
2. Soft-bodied organisms are less likely to leave recognisable remains than organisms with hard parts, so early life is poorly represented.
3. Even when fossils form, erosion, heat, pressure and geological movement can damage or destroy them.
4. Many surviving fossils are buried in inaccessible rocks or have not yet been discovered, so the available sample is incomplete.
5. The absence of a fossil from a particular layer therefore does not prove that the organism never lived at that time.
6. Gaps limit how confidently every stage can be reconstructed, while the overall record still provides evidence that organisms have changed.

Resistance shows evolution happening

1. A bacterial population may contain inherited differences that make some bacteria resistant to a particular antibiotic.
2. A random mutation can produce a resistant variant before exposure, without the antibiotic directing that useful change.
3. When the antibiotic is present, susceptible bacteria are killed or their reproduction is inhibited, while resistant bacteria are more likely to survive and reproduce.
4. The resistant bacteria copy their genetic material during reproduction and pass the resistance variant to descendants.
5. Their descendants form an increasing proportion of the population, so an inherited characteristic has become more common across generations.
6. This is observable evolution because it concerns a population changing over generations, rather than an individual becoming accustomed to the antibiotic.
7. Bacteria can pass through many generations in a short time, allowing the change to be observed much faster than many large changes represented in the fossil record.
8. Measurements of the resistant proportion over time are more informative than a final resistant count alone, especially if the total population size has changed.
9. Repeated observations support the conclusion more strongly than one sample because small samples can differ by chance.

Shared structures support ancestry

1. Homologous structures are structures with a common evolutionary origin that may now perform different functions.
2. The illustrated vertebrate limbs contain corresponding bones arranged in a shared basic pattern, although their proportions and uses differ.
3. A human arm, dog forelimb, bird wing and whale flipper are used differently, but their corresponding structures support descent from a common ancestor.
4. Together with evidence of change through time, inherited structural similarities help explain how related organisms can become different.

5.2.6 Darwin and Wallace

Darwin's observations

1. Charles Darwin developed an explanation of how species could change after comparing organisms, fossils and environments during and after his voyage on HMS Beagle.
2. He observed that organisms in different places shared similarities but also had differences associated with their surroundings.
3. Island organisms could resemble those on nearby mainland areas while possessing distinctive features, which raised questions about their origins.
4. Fossils also showed that some extinct animals resembled living animals from the same broad region.
5. These observations supported the possibility that species were related through common ancestry and had changed after populations became separated.
6. Darwin also studied variation in domesticated organisms, where breeders could increase the occurrence of inherited characteristics by choosing which organisms reproduced.
7. This helped him develop the idea that differences in survival and reproduction in nature could also change populations over generations.
8. The finch tree illustrates branching ancestry, with different descendant species traced back to shared ancestral populations.

Wallace and the joint announcement

1. Alfred Russel Wallace independently developed an explanation of evolution by natural selection while studying organisms and their geographical distribution.
2. His observations in tropical regions, including the Malay Archipelago, showed patterns in where related organisms lived.
3. Wallace sent Darwin an account of his ideas in $1858$, and their explanations were presented together to the Linnean Society that year.
4. Darwin and Wallace were not present at that meeting, so a joint presentation does not mean that they personally delivered it together.
5. Darwin published On the Origin of Species in $1859$, setting out an extended argument supported by observations and comparisons.
6. Both scientists are credited with identifying natural selection as a mechanism by which populations evolve.
7. Their shared explanation connected existing inherited variation with differences in reproductive success, making it possible to explain adaptation without assuming organisms change deliberately.

Evidence and acceptance

1. The theory challenged the widely held view that species were fixed and had been created separately.
2. Some objections reflected religious or cultural beliefs, while scientific questions concerned the evidence and the mechanism of inheritance.
3. Darwin had assembled substantial evidence, but the fossil record was incomplete and the genetics needed to explain inheritance was not yet established.
4. Neither Darwin nor Wallace could use knowledge of genes and DNA in the modern sense to explain how inherited variants were transmitted.
5. Later work on inheritance and mutations supplied that missing mechanism and strengthened the explanation of natural selection.
6. Further observations could be tested against the theory, allowing scientific confidence to develop as different lines of evidence supported the same explanation.
7. An earlier proposal by Lamarck suggested that the use or disuse of structures caused changes during life that could then be inherited.
8. The giraffe illustration represents that historical proposal: repeated stretching was supposed to lengthen the neck, with the acquired change passed to offspring.
9. The natural-selection explanation instead depends on inherited differences already arising within populations and different contributions to later generations.

Impact on modern biology

1. Evolution provides a connected explanation for adaptation, the diversity of organisms and the similarities shared by related groups.
2. It gives classification an evolutionary basis, because grouping organisms can aim to reflect ancestry rather than appearance alone.
3. It also supports predictions about how populations may respond to changing conditions, including the spread of inherited resistance.
4. Understanding that populations contain valuable genetic variation informs conservation, because preserving only a few genetically similar individuals may lose much of that variation.
5. These applications extend the impact of Darwin's and Wallace's ideas beyond explaining the origin of visible differences between organisms.

Seed banks conserve variation

1. Seed banks store living plant material so that species and genetic variants remain available for future growth.
2. Collections should represent many parent plants and, where appropriate, different populations, because seeds from a single parent do not capture all the variation in a species.
3. Collecting a representative sample increases the chance of retaining alleles associated with different environmental tolerances and other inherited characteristics.
4. Seeds are identified and labelled with their origin so that the stored material can be traced and used appropriately later.
5. For species whose seeds tolerate drying and cold storage, dry conditions reduce metabolic activity and low temperatures slow deterioration, extending the period of viability.
6. Stored seeds remain living and must be checked for viability, meaning their ability to germinate and grow under suitable conditions.
7. If a sample loses viability, fresh material may need to be collected or plants grown to produce replacement seeds while maintaining the collection's genetic diversity.
8. Stored seeds can help restore a plant population after local loss and provide material for research into inherited variation.
9. A seed bank cannot preserve every species in the same way, because some seeds are damaged by drying or freezing.
10. Seed storage also does not maintain all the interactions of a living habitat, so it supports conservation of wild populations rather than replacing habitat protection.