Unit 3 — Variation of Traits in Living Organisms

• Look at a family photograph.
• Children resemble their parents in some features and differ in others.
• Genetics is the science that explains these similarities and differences by studying how genetic information passes from parents to offspring.

• The genetic information is stored in a chemical substance called the genetic material, deoxyribonucleic acid (DNA).
• In a cell, the genetic material is in the nucleus.
• A DNA molecule is extremely long, so it is coiled around protein molecules to form thread-like chromosomes.
• The genetic material of a chromosome is divided into sections; each section is a gene.

A gene is a segment of the genetic material (DNA) that carries the information responsible for a specific inherited trait, such as eye colour, hair texture or height.

So: cell → nucleus → chromosomes → genes (DNA).

• Inherited traits are transferred from parents to children through genes carried by the gametes: the sperm (male gamete) and the ovum or egg (female gamete).
• Gametes are produced in the gonads (testes and ovaries) by a type of cell division called meiosis.
• Each gamete contains only half of the genetic material, so it carries only one copy of each gene.
• At fertilisation, the nucleus of the sperm fuses with the nucleus of the ovum, so the new individual has two copies of every gene: one from the father and one from the mother.

Look at a table of eye colour in four people:

• When the two copies are identical (persons A and D) the trait is clearly brown or blue.
• When the two copies are different (B and C), the eyes are still brown.
• So the brown copy is dominant over the blue copy, and the blue copy is recessive.

Definitions:

• Allele: each of the different forms of the same gene. A gene can have more than two alleles (for example eye colour: brown, blue, green; hair colour: blond, red, brown, black).
• Each individual usually has two alleles for each trait, one from each parent.
• Dominant allele: the allele whose effect appears in the organism when two different alleles are present.
• Recessive allele: the allele whose effect is completely masked in the presence of a dominant allele; it appears only when two copies are present.
• Principle of complete dominance: when the dominant trait appears and completely masks the contrasting trait.
• Homozygous (pure): two identical alleles (BB or bb). Heterozygous (hybrid): two different alleles (Bb).
• Phenotype: the observable inherited trait (e.g. brown eyes).
• Genotype: the genetic makeup, i.e. the alleles carried (e.g. Bb).

Symbols. The dominant allele is written as a capital letter (first letter of the trait), the recessive allele as the same small letter. For eye colour: B = brown (dominant), b = blue (recessive).

• Notice: two people with the same phenotype (brown eyes) can have different genotypes (BB or Bb).
• A recessive trait appears only when the genotype is bb.
• A difference in genotype (cause) can produce a difference in phenotype (effect).

In the nineteenth century the scientist Gregor Mendel (1822–1884) carried out systematic experiments on pea plants. Why peas?

• They show clear, contrasting traits that are easy to tell apart: seed colour (yellow/green), seed shape (round/wrinkled), plant height (tall/short), flower colour (purple/white), flower position (axial/terminal), pod shape (inflated/constricted), pod colour (green/yellow).
• Pollination can be controlled easily.

• Mendel crossed (hybridised) plants that differ in one trait after making sure each parent was purebred (always gave the same trait).
• Analysing his results he concluded that inherited traits do not appear at random but follow regular patterns that can be explained scientifically and used to predict the probability of traits in offspring.
• This was the foundation of modern genetics.

Pairs of contrasting traits in pea plants (dominant / recessive):

Genetic notation: P = parents; ♂ = male; ♀ = female; × = cross; G = gametes; F₁ = first generation; F₂ = second generation.

When two purebred individuals that differ in one pair of contrasting traits are crossed:

• all individuals of the first generation (F₁) show only one of the parents' traits, the dominant one (100%);
• when F₁ individuals are crossed with each other, both traits appear in F₂ in the ratio 3 (dominant) : 1 (recessive).

Explanation.

• Each trait is controlled by a pair of alleles.
• During gamete formation the two alleles of the pair separate (segregate), so each gamete carries only one allele.
• At fertilisation, an allele from the father and one from the mother come together to form a new pair.

Example: seed colour (Y = yellow, y = green)

P: pure yellow (YY) × green (yy) Gametes: Y and y F₁: all Yy (yellow), 100% F₁ × F₁: Yy × Yy; gametes Y, y (each parent)

Punnett square:

F₂ genotypes: 1 YY : 2 Yy : 1 yy. F₂ phenotypes: 3 yellow : 1 green. Probability of green seeds = 1/4 = 25%.

A Punnett square is a tool for predicting the possible genotypes and phenotypes of the offspring of a particular cross.

How to build one:

1. Work out the gametes each parent can make; the number of boxes depends on the number of gamete types.
2. Draw a grid of rows and columns.
3. Write the gametes of one parent across the top, and the gametes of the other parent down the left side.
4. Fill each box by combining the allele above with the allele at the side.
5. Count genotypes and phenotypes and give the ratio or percentage.

Worked example 1: purple × white (Check your understanding)

Purple (P) is dominant over white (p). Cross pure purple PP × white pp. Gametes: P and p. F₁: all Pp, purple (100%). F₁ × F₁: Pp × Pp

F₂: 1 PP : 2 Pp : 1 pp, i.e. 3 purple : 1 white (75% purple, 25% white).

Worked example 2: a heterozygous axial plant × a terminal plant

A = axial (dominant), a = terminal. Cross Aa × aa. Gametes: A and a (from Aa); a only (from aa).

Offspring: 2 Aa : 2 aa → 50% axial (Aa), 50% terminal (aa); phenotype ratio 1 : 1. Such a cross (with a homozygous recessive) is useful for finding out whether a dominant-looking plant is pure or hybrid.

Worked example 3: unknown purity

A tall pea plant (T = tall, t = short) is crossed with a short plant. Half of the offspring are short. What is the genotype of the tall parent? Short offspring are tt, so each parent gave a t; so the tall parent must be Tt (heterozygous). If the tall parent had been TT, all offspring would have been tall.

• When two purebred individuals that differ in two or more pairs of contrasting traits are crossed, each pair of traits is inherited independently of the others.
• Analysed separately, each trait appears in F₂ in the ratio 3 : 1.

The dihybrid cross: seed shape and seed colour

R = round (dominant), r = wrinkled; Y = yellow (dominant), y = green. P: pure round yellow (RRYY) × wrinkled green (rryy) Gametes: RY and ry F₁: all RrYy, round yellow (100%) — both dominant traits appear.

F₁ × F₁: RrYy × RrYy. Each parent produces four types of gametes with equal probability: RY, Ry, rY, ry. Fusion gives 16 combinations:

Count of phenotypes in F₂ (out of 16):

• round yellow (both dominant): 9
• round green (first dominant, second recessive): 3
• wrinkled yellow (first recessive, second dominant): 3
• wrinkled green (both recessive): 1

Phenotype ratio 9 : 3 : 3 : 1.

Check each trait alone: round = 9 + 3 = 12, wrinkled = 3 + 1 = 4 → 12 : 4 = 3 : 1. Yellow = 9 + 3 = 12, green = 3 + 1 = 4 → 3 : 1. So shape is inherited independently of colour.

Worked example 4 (check your understanding)

T = tall, t = short; G = green pod, g = yellow pod. Two plants heterozygous for both traits (TtGg × TtGg) are crossed. What fraction are tall with green pods? From the 9 : 3 : 3 : 1 pattern, tall green = 9/16 (56.25%). You can also multiply independent probabilities: P(tall) = 3/4 and P(green) = 3/4, so 3/4 × 3/4 = 9/16.

Worked example 5: a test cross in humans

• Curly hair (H) is dominant over straight (h); brown eyes (B) dominant over blue (b).
• A man with curly hair and brown eyes (HhBb) marries a woman with straight hair and blue eyes (hhbb).
• Man's gametes: HB, Hb, hB, hb.
• Woman's gametes: only hb.

Phenotypes: curly brown : curly blue : straight brown : straight blue = 1 : 1 : 1 : 1 (25% each).

Every person has a unique genetic makeup (except identical twins). This variation arises because:

• there are different alleles for the same gene;
• the alleles are distributed randomly among gametes when they are formed;
• gametes from the two parents combine by chance at fertilisation.

• So even brothers and sisters differ in some traits.
• This genetic diversity helps a species adapt to different environmental conditions and survive over time.

• Sometimes a gene carries a mutation (a change) that causes a disease.
• Such a disease is a genetic disease; it can appear from birth or later in life, and it can be passed to the next generation.

In many inherited diseases the disease-causing allele is recessive. Let N = normal allele and n = disease allele:

• NN: healthy, not a carrier.
• Nn: healthy-looking, but a carrier: has one copy of the disease allele but shows no symptoms; can pass it on.
• nn: has the disease (two disease alleles, one from each parent).

Worked example 6: two carrier parents

Both parents are Nn (carriers). Punnett square:

• Healthy, not carrier (NN): 25%
• Healthy carriers (Nn): 50%
• Affected (nn): 25% So each child of two carriers has a 1 in 4 chance of the disease, even though both parents look healthy. This answers "Why can a child be affected though both parents appear healthy?"

Worked example 7: one carrier, one normal

Nn × NN → 50% NN and 50% Nn. No child is affected, but half are carriers.

Worked example 8: carrier × affected

Nn × nn → 50% Nn (carrier) and 50% nn (affected).

Examples of recessive inherited diseases:

• Thalassaemia (Mediterranean anaemia): affects the production of haemoglobin and causes anaemia of varying severity.
• Galactosaemia: the body cannot break down the sugar galactose; babies suffer vomiting, yellowing of skin and eyes, and poor growth.

• Relatives share some genes they inherited from common ancestors.
• If one of these genes causes a disease, the probability that both partners are carriers of the same disease allele is higher in relatives than in unrelated couples.
• When both carry the same recessive allele, the chance of an affected child (1 in 4) increases.
• For this reason health authorities recommend:

• pre-marital medical screening for certain inherited diseases;
• genetic counselling: specialists study the family's medical history, run genetic tests and advise couples about the risks, which protects families and reduces the spread of diseases;
• comprehensive genetic screening: modern techniques that examine thousands of genes at the same time, helping early detection of rare diseases.

• DNA → chromosome → gene; gametes carry one copy, zygote two.
• Alleles, dominant/recessive, homozygous/heterozygous, genotype/phenotype.
• Mendel's first law: segregation; 100% dominant in F₁ and 3 : 1 in F₂.
• Mendel's second law: independent assortment; 9 : 3 : 3 : 1 in F₂.
• The Punnett square predicts offspring.
• Recessive genetic diseases appear when both alleles are the disease allele; carriers look healthy; relatives' marriage raises risk; screening and counselling reduce it.

• To understand the life of organisms in an ecosystem it is not enough to study one individual; we study populations.
• A population is a group of individuals of the same species, able to reproduce with each other, living in the same place at the same time.

• Populations are not static.
• The number of individuals in some species stays steady for long periods; in others there is a rapid rise or a sudden collapse.
• This shows the interaction between organisms and environmental factors.

Imagine a few rabbits introduced to a new place that has plenty of food and no competitors:

1. At first, the rabbits adjust to the new place.
2. They begin to reproduce.
3. With abundant food, the population rises quickly.
4. As numbers rise, food begins to run out.
5. Competition increases and the growth slows down.
6. The population reaches a relatively stable size balanced with its environment.

The growth curve has four phases: lag phase (slow start), exponential growth phase (rapid increase), slowing-down phase, and stationary phase (at the carrying capacity).

Exponential growth. Under ideal conditions a population can multiply rapidly: 2 → 4 → 8 → 16 → 32 …, i.e. 2¹, 2², 2³, 2⁴, 2⁵ …

Worked example 1

A culture of bacteria doubles every hour starting from 1 cell. After 1 hour: 2 cells (2¹); after 2 hours: 4 (2²); after 5 hours: 2⁵ = 32; after 10 hours: 2¹⁰ = 1024 cells. If it starts from 3 cells, after 4 hours there are 3 × 2⁴ = 48 cells.

Environmental resistance.

• In nature, growth cannot go on for ever because resources (food, water, space) are limited.
• The factors that limit population growth are called environmental resistance:

• depletion of resources,
• increased competition among individuals,
• fast spread of diseases and parasites (and predators).

• Because of environmental resistance, the population stops growing at the carrying capacity: the maximum number of individuals of a species that an environment can support continuously without damaging its resources.
• If a population goes above the carrying capacity, resources are exhausted, so deaths exceed births and the number falls back.

Application. In nature reserves, scientists determine the carrying capacity of each species and intervene if a population grows too much or declines sharply, to maintain the balance of the ecosystem.

Two main groups:

• 1.
• Environmental factors. All living (biotic) and non-living (abiotic) components of the environment: food, water, temperature, disease, predators and space.

• When the environment is rich (plenty of resources), survival and reproduction increase and the population rises.
• When it deteriorates (scarcity, danger, pollution), the population decreases due to lower reproduction, higher death rate, or both.

• 2.
• Genetic factors. The inherited traits that affect an organism's ability to adapt, survive and reproduce.
• Individuals in a population are not identical; the genetic variation gives some a better chance in a given environment.
• Examples: fur colour, resistance to disease, tolerance of heat or cold, sharp eyesight, strong sense of smell, strong beaks for cracking seeds.

Classifying cases:

Resource abundance followed by scarcity: the population first increases, then, as resources run short, competition rises and the population falls until a balance with the available resources is reached.

Natural selection

• explains how populations change (evolve) over time.
• Individuals that have inherited traits suited to their environment are more likely to survive and reproduce than individuals without those traits.
• These useful traits are passed to the offspring and become more common in each generation.

Important points:

• The environment does not give the organism new traits. It selects, among the traits that individuals already have, those that help survival.
• Better-adapted individuals live longer and leave more offspring.
• Less adapted individuals are more likely to die before reproducing or reproduce less.
• Over many generations the proportion of useful traits rises, while the proportion of less useful traits falls.

Example: peppered moths and lichens

• Before the Industrial Revolution in Europe, tree trunks were light-coloured and covered with lichens.
• Light-coloured moths were hard for predators (birds) to see on them, so they survived more often.
• After the Industrial Revolution, air pollution killed the lichens and darkened the trunks.
• Now light moths were easy to see and were eaten, while dark moths were hidden.
• Over time dark moths became common and light moths became rare.

Explanation using natural selection: (1) the moths were already varied in colour (variation); (2) the changed environment made the dark colour an advantage; (3) dark moths survived and reproduced more; (4) they passed the dark-colour allele to their offspring; (5) the proportion of dark moths rose over generations.

• Lichens as indicators. Lichens are formed by a fungus living with an alga or cyanobacterium.
• They are sensitive to air pollution, so their presence or absence shows the quality of the air.

Worked example 2: a mathematical model of selection

A population has 100 rabbits: 60 fast and 40 slow. After predation, 50 fast and 10 slow rabbits remain.

• Fast rabbits surviving: 50/60 = 83.3%. Slow rabbits surviving: 10/40 = 25%.
• Before: fast = 60% of the population. After: total = 60 survivors; fast = 50/60 = 83.3% of the population.
• Conclusion: the fast trait is selected for. If the survivors breed, the next generation will contain more fast rabbits. Repeating this over generations makes the fast trait common: natural selection is a cumulative process.

Worked example 3: adaptation to the cold

In a cold region, animals with thick fur lose less heat. Suppose in a population of 200 animals, 120 have thick fur and 80 thin fur. A very cold winter kills 10% of the thick-fur animals and 50% of the thin-fur animals. Survivors: thick: 120 − 12 = 108; thin: 80 − 40 = 40. Total survivors: 148. Thick fur is now 108/148 = 73% (up from 60%). The trait that helps survival has become more common.

Artificial selection is the process in which humans select plants or animals with desirable traits and breed them so that the offspring show these traits more strongly.

• Example: a farmer chooses the cows that give the most milk and breeds them.
• Their offspring are more likely to give a lot of milk.
• Repeating this over generations raises the average milk production.

More examples: plants that produce larger fruit; cattle with more meat; hens that lay more eggs; dogs with chosen shape or behaviour.

Stability and change. Organisms keep some inherited traits for long periods, while others change with the environment or because of selection.

Humans want to keep useful traits to improve production, protect superior breeds and support food security. Two kinds of techniques:

1. Traditional techniques: crossbreeding good breeds, and choosing the best plants for cultivation.
2. Modern techniques: preserving gametes (sperm, eggs) and tissue culture (growing whole plants from small pieces of plant tissue). Tissue culture produces disease-free plants and supports research and treatment; gene banks store gametes, cells and valuable breeds for research, treatment and the protection of biodiversity.

Discussion:

• artificial selection improves breeds and production, but it can also reduce genetic diversity.
• If all individuals are genetically similar, a single disease or environmental change could affect all of them, and the population might disappear.
• Therefore breeders and gene banks aim to keep a balance between improvement and diversity.

• A population is a group of the same species in the same place and time.
• Growth: lag, exponential, slowing, stationary at carrying capacity; limited by environmental resistance.
• Factors: environmental and genetic.
• Natural selection: the environment selects the favourable inherited traits; slow and cumulative.
• Artificial selection: humans choose the traits; faster; may lower genetic diversity.
• Traditional and modern techniques preserve desirable traits.

1. Confusing the genotype with the phenotype. "Brown eyes" is a phenotype; "Bb" is a genotype. Always say which one you are describing.
2. Thinking a dominant allele is "stronger" or more common. Dominance only describes which allele shows in a heterozygote. A dominant allele can be rare in a population.
3. Writing gametes with two alleles. A gamete carries only one allele of each gene. For Yy the gametes are Y and y, never "Yy". For RrYy each gamete carries one allele of each gene: RY, Ry, rY or ry.
4. Forgetting that ratios are probabilities. A 3 : 1 ratio does not mean that a family of four children must have exactly three dominant and one recessive child. Each child has a 75% chance of showing the dominant trait, independent of the previous child.
5. Mixing up carriers and patients. A carrier (Nn) is healthy but can pass on the disease allele; a patient (nn) shows the disease.

Each birth is an independent event. If two carrier parents have a 25% chance of an affected child, then after a first affected child the chance of the second child being affected is still 25%. To find the chance of two particular outcomes in two separate children, multiply: chance of two affected children in a row = 1/4 × 1/4 = 1/16.

• A pea plant with round seeds is crossed with a plant with wrinkled seeds.
• In the offspring, 48 plants have round seeds and 52 have wrinkled seeds (close to 1 : 1).
• What are the genotypes of the parents?
• A 1 : 1 ratio appears in a cross between a heterozygote and a homozygous recessive: Rr × rr.
• The wrinkled offspring (rr) prove that the round parent had an r allele, so it was Rr.

If two hybrid tall pea plants (Tt × Tt) produce 400 seeds that all grow, about how many plants are expected to be short? Short = tt = 1/4 of 400 = 100 plants; tall = 300 (of which about 100 are TT and 200 are Tt). Real counts usually differ a little from the expected numbers because fertilisation is a matter of chance, but with large numbers the results come close to the predicted ratio. That is why Mendel's use of hundreds and thousands of plants gave clear results.

• Genes (DNA) are the cause; the inherited traits are the effect.
• Variation within a population (different alleles) is the raw material on which natural selection works. Without variation there is nothing to select.
• Artificial selection uses the same variation, but the human breeder decides which individuals reproduce.
• Genetic diseases show what can happen when a harmful recessive allele becomes homozygous; communities reduce this through awareness, screening and counselling, which also respects human differences and protects the health of future generations.