BIOL10010 - Foundational Biology - Life's Complexity

What is evolution?

The cumulative change in the genetic composition of a population or species over time

What are the three major propositions for evolution?

1. Species are not immutable: populations show phenotypic variation and species can change over time

2. Descent with modification: related species with a common ancestor diverge from one other gradually over time (but structures remain homologous, or related)

3. Natural selection: differences in the phenotypes of individuals cause some of them to survive and reproduce more effectively than others and therefore outcompete them

What is macroevolution?

Explains evolutionary changes among large taxonomic groups above the species level, including the origin, diversification and extinction of species over time

What is microevolution?

Explains evolutionary changes within species that can be observed directly acting upon natural populations

What is a monophyletic group in a phylogeny?

Includes the common ancestor and all descendants (a 'clade')

What is a polyphyletic group in a phylogeny?

Does not include the common ancestor

What is a paraphyletic group in a phylogeny?

Includes the common ancestor, but not all descendants

What is convergent evolution?

Distantly related organisms independently evolve similar traits in order to adapt to their environment

What are the six agents of change underlying evolution?

1. Mutation

2. Genetic drift

3. Natural selection

4. Recombination

5. Non-random mating

6. Gene flow

Describe how mutation may arise through DNA replication

1. Through DNA replication, DNA polymerase adds to the 3' end of the new strand

2. It should add the complementary nucleotide of the nucleotide on the original strand

3. Occasionally, however, there is a misincorporation error

Describe how mutation may arise through DNA damage

1. Exogenous sources:

- UV radiation

- Gamma and X-rays

- Chemical mutagens

2. Endogenous sources:

- Reactive oxygen species

- Hydrolysis

- Endonucleases

- Alkylation

**Although enzymes repair these damages, they may not be replaced with the original nucleotide

What are the common different types of mutation?

1. Point mutation: single base change from one nucleotide to another

2. Insertion: a segment of DNA is inserted into the middle of an existing sequence, could be a single base or as long as thousands of bases, including entire genes

3. Deletion: a segment of the DNA may disappear, or the entire gene may be removed

4. Frameshift mutation: any mutation (insertion or deletion etc) that shifts the reading frame of the entire sequence, changing the amino acid sequence of the protein

What are examples of rarer but larger changes in mutations?

1. Gene duplication: duplication of whole genes

2. Genome duplication: duplication of all chromosomes

3. Inversion: regions of the DNA are removed, flipped, and then placed back into its original spot

4. Chromosome fusion: chromosomes are joined together

5. Aneuploidy: Lost or gain of chromosomes

What are the characteristics of germline mutations?

1. Affects gametes (sperm, eggs)

2. Creates new variation (alleles) and can be heritable

3. Entire organism carries the mutation

4. Half the gametes of offspring will carry the mutation

What are the characteristics of somatic mutations?

1. Affects the daughter cells of a single cell

2. Not heritable (but can be passed down in plants through vegetative reproduction)

3. Only specific areas of the organism carries the mutation

4. None of the gametes of the offspring will carry the mutation

What are the consequences of mutations?

1. No phenotypic effect (neutral)

2. Deleterious (negative)

3. Advantageous (positive)

What is genetic drift?

The random sampling of alleles across generations, and is more influential in small populations

What is natural selection?

The process whereby organisms better adapted to their environment, due to having advantageous mutations, survives and produces more offspring

What are examples of non-random mating?

1. 'Alpha' male organisms gaining more reproductive access

2. Many plants tend to self-pollinate rather than outbreed

3. Some plants have flowering time polymorphisms

Describe assortative mating with examples

Individuals are more likely to breed with others who have the same phenotype for a particular gene

1. Red flowers pollinate with red flowers and purple with purple, due to preference of pollinators

2. Large snails are more likely to breed with large snails, and small snails with small snails

What is gene flow?

The spread of genetic variation across geographical areas due to migration, hybridisation or gamete dispersal

How is the impact of gene flow calculated?

delta p = m * (f(A) migrants - f(A) residents)

Impact of gene flow = (level of migration, movement or hybridisation as a percentage) x (difference in allele frequency)

How does recombination lead to allele variation?

When multiple genes are involved for one phenotype or for multiple phenotypes, recombination allows for every gamete to have a different combination of alleles (as chromatids will no longer be identical preceding meiosis 2)

What is the purpose of the Hardy-Weinberg theorem?

Provides the expected relationship between alleles, genotypes and phenotypes in diploid populations

What is the Hardy-Weinberg formula to calculate genotype frequencies using allele frequencies?

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

p = frequency of dominant allele

q = frequency of recessive allele

What is the Hardy-Weinberg formula to calculate allele frequencies using genotype frequencies?

p = f (AA) + 1/2 * f(Aa)

q = f (aa) + 1/2 * f(Aa)

OR

q = Root of q^2 = Root of f (aa)

Then

p = 1 - q

BUT second method is only accurate under Hardy-Weinberg equilibrium

What are the five assumptions of the Hardy-Weinberg equilibrium?

1. No gene flow

2. No mutation

3. Infinite population size

4. Random mating

5. Equal fitness (no selection)

How can we determine if a population is in Hardy-Weinberg equilibrium?

1. Calculate allele frequencies using population genotypes, via the formulae p = f (AA) + 1/2 * f(Aa) and q = f (aa) + 1/2 * f(Aa)

2. Use the Hardy-Weinberg equation p^2 + 2pq + q^2 = 1 to calculate the expected genotype frequencies, if the population is in Hardy-Weinberg equilibrium

3. Apply a simple chi-squared test: Find difference between observed and expected values for all three genotypes, square each of them, divide each by the expected value, then add them up to obtain the X^2 value

What is speciation?

The evolutionary process by which new species arise through reproductive isolation. Speciation causes one evolutionary lineage to split into two or more lineages.

What is the difference between allopatric and sympatric speciation?

Allopatric speciation occurs when an ancestral population is divided by a physical barrier, whereas sympatric speciation occurs when an ancestral population is divided without geographic barriers

Describe how speciation can occur via fixation of alleles

1. Two lineages from the same ancestral population becomes physically separated from each other (no gene flow)

2. Both genes develop independently, and new alleles becomes fixed in each descendant lineage but at a different locus

3. Neither of the alleles are incompatible with the ancestral alleles, but the two new alleles in the two different genes are incompatible with each other, hence the two lineages are reproductively isolated

Describe how speciation can occur via chromosomal rearrangements

1. Two independent chromosome fusions occur in two sister lineages

2. Neither centric fusion by itself results in difficulties at meiosis

3. However, when the centric fusions become fixed, the hybrids formed between these two lineages will become sterile, because the chromosomes will not be able to pair normally during meiosis in hybrids

What does it mean if an allele is fixed?

All individuals in the population or species are homozygous for that version

Distinguish between prezygotic and postzygotic isolation

Prezygotic isolation is when barriers to reproduction act before the union of the nuclei of the two gametes, whereas postzygotic isolation is when barriers to reproduction act after the union of the nuclei of the two gametes

What are examples of prezygotic isolation?

1. Geographical isolation (e.g. separation of populations)

2. Mechanical (e.g. pollinators pollinating specific species)

3. Behavioural (e.g. courtship calling with different sounds)

4. Mating time differences (e.g. different flowering times)

5. Ecological differences (e.g. preferences for different ecological niches, such as certain rocks, deep areas etc)

What is an example of postzygotic isolation?

The fertilised egg or the offspring is inviable (sterile)

What is the 'Biological Species Concept'?

Defines species as a group of actually or potentially interbreeding natural populations that produce fertile offspring

What is adaptive introgression?

Inheritance of beneficial variation from related species, via hybridisation, that accelerate adaptation to, and survival in new environments

What are hybrid zones?

An area where two closely related species cohabit and interbreed

How many hybrid zones influence the involved species?

1. Reinforcement: strengthens reproductive barriers, decreasing incidence of hybrids

2. Fusion: weakens reproductive barriers, until two species become one

3. Stability: hybrids continue to survive and reproduce

What is balancing selection?

Balancing selection maintains genetic diversity in a population by keeping alleles at frequencies higher than expected by chance

1. Negative frequency dependent selection

2. Heterozygote advantage

What is negative frequency dependent selection?

Occurs when rare phenotypes have higher fitness than common phenotypes

What is heterozygote advantage?

Occurs when heterozygous individuals have higher fitness than homozygous individuals

What is relative fitness (w)?

Describes the success of a genotype, rather than an organism. Relative fitness is standardised by the success of other genotypes in the population and ranges from 0 to 1.0.

What is sexual selection?

The selection for traits which enhance mating or fertilisation success, often at the expense of survival

What is intersexual selection?

1. Non-random mating involving mate choice

2. One sex holds preference for specific traits (ornaments) in another

3. These ornaments are costly to bear, so they are honest signals of mate quality

4. Hence, ornaments will become exaggerated until balanced by natural selection (as these ornaments reduce survival)

What is intrasexual selection?

1. Non-random mating involving male-male competition

2. Individuals of the same sex compete for access to mates via physical combat, displays of strength and territorial battles

3. Traits that increase strength and competition (armaments) are highly preferable, but are costly to bear and to use

4. Hence, armaments will become exaggerated until balanced by natural selection (as these armaments reduce survival)

What are examples of sexual selection after mating?

1. Cryptic female choice: evolution of female ability to eject sperm from low-quality males

2. Sperm competition: evolution of male ability to remove sperm present in the female, to ensure that his sperm fertilises all the eggs

Explain how sexual conflict influences selection

Sexual conflict occurs when reproductive interests of the sexes diverge, resulting in adaptations which manipulate the opposite sex, which in turn further results in counter-adaptations from the opposite sex

What is coevolution?

The process that occurs when two or more species affect each other's evolution by exerting selective pressures on each other

What is the Red Queen Hypothesis?

The hypothesis that species must constantly adapt and evolve in order to survive while pitted against ever-evolving species

What are antagonistic interactions in coevolution?

Interactions causing organisms to coevolve in response to the predatory actions of the other species

1. Predator-prey

2. Plant-herbivore

3. Host-parasite

What are mutualistic interactions in coevolution?

Interactions causing organisms to coevolve in a way that will benefit both organisms

1. Plant-pollinator/disperser

2. Cleaning

3. Endosymbiosis

How can amino acid sequence in genomes be used to trace phylogenies?

Amino acid sequences can undergo alignment (typically using a computer software) and then comparisons between each character (amino acid) can be made to assert homology

What are the different types of phylogenetic trees?

Cladogram: shows just the clades (topology)

Phylogram: branch length is proportional to number of changes

Ultrametric: uses a real time axis, terminal roots align

What is population structure?

Arises when demographic processes produce systematic differences in allele frequencies between subsets of a larger population

List some factors which may result in high population structure

1. Population divergence a long time ago

2. Small but stable population sizes

3. Geographic isolation; no interactions between subsets

What are the benefits of aerobic respiration?

- Releases more ATP molecules than anaerobic respiration (32-38 ATP vs 2 ATP)

- May have allowed for the evolution of multicellularity and larger organism size

What are the benefits of anaerobic respiration?

- Quickly releases energy

- Can occur in low oxygen environments

What are the essential features of exchange surfaces?

1. Large surface area to volume ratio

2. Thin, small diffusion pathway

3. Partially permeable

4. Movement of external medium e.g. air

5. Movement of internal medium e.g. blood

What are the factors involved in Fick's Law?

1. Surface Area

2. Partial Pressure Gradient

3. Diffusion Coefficient

4. Diffusion Distance

What are the features in plants which facilitates gas exchange?

1. Stomata (mostly in leaves)

2. Lenticels (in woody stems and shoots)

2. Aerenchyma (tissues forming air spaces)

3. Living cells live close to surface

How do wetland plants (submerged below water) obtain oxygen from the air?

Living stems often form horizontal roots called rhizomes which are connected to broken (dead) stems. They can use these broken stems as a 'snorkel' to intake carbon dioxide and discharge oxygen.

How do fungi respire?

- Alternates between aerobic and anaerobic respiration

- Mycelium (roots) of fungi contains microscopic hyphae which extends out into small air pockets in the soil

- Fruiting body (top) of fungi have very thin walls for gas exchange with the air

How do smaller organisms optimise gas exchange?

Maintaining a high body surface area to volume ratio via flat, porous, hollow or other unique shapes

How do larger organisms optimise gas exchange?

Specific gas exchange surfaces

1. External gills

2. Internal gills

3. Lungs

4. Tracheae

What are the two processes that ensure sufficient gasses are exchanged with the environment in animals?

1. Ventilation; gases are moved across the gas exchange surface, ensuring an optimal pressure gradient

2. Circulation; gases are moved to/from the gas exchange surface to/from the body tissues

Describe the respiratory structure of the tracheae

Network of tubes which extends and provides oxygen throughout the body.

- Spiracles (opening) --> Tracheae --> Tracheole

- Spiracles can be closed to prevent water loss

- Abdomen can be contracted to increase ventilation and suck more air and oxygen inside

Describe the respiratory structure of the lungs

Contains small capillaries which transport oxygen to and carbon dioxide from the body tissues

- Trachea --> Bronchi --> Bronchioles --> Alveoli

- Large surface area for gas exchange

- Kept moist by surfactants (contains hydrophilic and hydrophobic end, reducing surface tension between air space and alveoli)

Describe the structure of the lungs in birds which facilitates gas exchange

1. Lungs do not move, but are instead ventilated by air sacs which pump air to and from the lungs in different specific orders

2. As a result, fresh air passes over the gas exchange surfaces during both inhalation and exhalation, resulting in a continuous supply of fresh air

3. Contains parabronchi within the lungs, further increasing surface area, and directly interacts with a large capillary network to effectively transport gases around the body

Describe the respiratory structure of the gills

1. Made up of many individual filaments covered in lamellae to increase surface area

2. As water flows over the gill surfaces and the individual lamellae, oxygen diffuses in and carbon dioxide diffuses out

3. All the lamellae on the gill are connected to the capillary system

Describe why the internal gills of fishes are so efficient

Countercurrent exchange mechanism:

Water and blood flows in opposite directions along the lamellae, maintaining the most favourable concentration gradient throughout the gill

What is the difference between autotrophs and heterotrophs?

Autotrophs are organisms capable of producing the majority of their food sources themselves, whereas heterotrophs must obtain their food from consuming other organisms

What are the two main autotrophic adaptations for producing food?

1. Photosynthesis (harness of sunlight)

2. Chemosynthesis (oxidation of inorganic compounds)

Describe the process of sulphur chemosynthesis

1. Occurs in oxygen-limited environments such as deep sea hydrothermal vents, by symbiotic bacteria and archaea etc.

2. Hydrogen sulphide is oxidised to form sulphite, theosulphate and elemental sulphur, producing ATP

3. ATP is required for carbon fixation, which can occur via the Calvin Cycle or the Reductive Carboxylic Acid Cycle, ultimately converting CO2 to glucose

What are the four main heterotrophic adaptations for consuming food?

1. Collection and capture of food

2. Mechanical digestion

3. Chemical digestion

4. Absorption

List some examples of heterotrophic adaptations for non-mobile plants and fungi

1. Fungi producing strong digestive chemicals to break down dead or decaying matter

2. Parasitic plants being able to invade the vascular tissues of other plants, stealing their nutrients

3. Carnivorous plants exhibiting physical and chemical signals to attract, capture and digest prey (e.g. exudate in digestive enzymes)

List some examples of heterotrophic adaptations for mobile animals

1. In vertebrates, specialised teeth in certain parts of the mouth to undergo specialised functions

2. Tongue of insects specialised to reach nectar from plants

3. Adaptations of the limbs, such as development of sharp claws in birds, to capture prey

What are essential nutrients for plants?

1. Macronutrients: phosphorus, sulfur, nitrogen, hydrogen, potassium, magnesium, calcium

2. Micronutrients: chlorine, iron, zinc, copper, manganese, boron, nickel

What happens if a plant does not receive enough nutrients?

Chlorosis: yellowing of leaves

What are essential nutrients for animals and how are they processed?

1. Carbohydrates: enters glycolysis, the citric acid cycle and oxidative phosphorylation pathway

2. Proteins: undergoes deamination and enters glycolysis or citric acid cycle pathway

3. Lipids: glycerol is phosphorylated and enters glycolysis, fatty acid chains undergo beta oxidation into Acetyl CoA which then enters the citric acid cycle

Describe the role of rhizobacteria in plant growth and nutrition

1. Produce antibiotics to protect the plant

2. Absorb unwanted chemicals from the soil

3. Facilitates the acquisition of essential nutrients

How does rhizobacteria aid the plant's uptake of nitrogen?

The bacteria converts atmospheric nitrogen to ammonia, which is then modified to ammonium or nitrate, which can then be taken up or used by plants

Describe the role of mycorrhizae in plant growth and nutrition

1. Accesses soil stores of nutrients that would otherwise be unavailable to the plant (e.g. phosphate, copper, zinc)

2. Acts as a physical barrier against pathogens

3. Produces antibiotics to protect the plant

What are the ways in which plants remove waste?

1. Transpiration via the stomata or lenticels

2. Urea from protein catabolism

3. Shedding of tissues and cells, carrying waste (amino acids, mineral salts, water) in vacuoles

4. Guttation; secretion of xylem sap containing water and mineral wastes from leaf margins

When does guttation occur?

- Typically at night, when stomata is closed to prevent water loss, causing root pressure to build up due to a lack of transpiration

- When root pressure exceeds transpiration, this is what ultimately drives the process of guttation

How does guttation excrete xylem sap and what structure is directly involved in this process?

Xylem sap containing excess water and minerals are secreted via secretory cells in the leaf epidermis called 'hydathodes', which are believed to have evolved from the modified stomata

How do fungi absorb nutrients?

- Small nutrients, such as sugars and amino acids, accumulate in a watery film surrounding the hyphae or yeast and diffuse into the cell wall

- Macromolecules and insoluble polymers, such as proteins and starches, undergo preliminary digestion via enzymes in the fungal exudate, before diffusing into the cell wall

How does the digestive tract of herbivores aid digestion?

1. Muscular stomach in herbivores, so that food can be squeezed and churned

2. Stomach contains acids and digestive enzymes, and mixing is assisted by the squeezing and churning

3. Some vertebrates (ruminants) have further specialised extensions of the stomach to prolong this process

Describe the process of rumination and fermentation

1. In ruminants, the stomach is split into four compartments (rumen, reticulum, omasum and abomasum)

2. The herbivore can regurgitate their food from their rumen back into their mouth for further mechanical digestion

3. The food then passes through the different compartments where the plant matter is fermented by the assistance of an array of microbes

How does the digestive tract of carnivores aid digestion?

1. Teeth adapted for hunting and killing prey, as meat tissues are effectively digested via chemical digestion rather than mechanical

2. Stomach and foregut highly acidic for the chemical digestion of proteins

3. Lipids are digested and absorbed in the midgut, where special bile is secreted

Describe the process of how waste is secreted in animals

Excess nitrogen in the body forms ammonia, which is highly toxic and must be removed from the body

1. Most aquatic animals directly releases ammonia into the environment, using diffusion and very little energy

2. Mammals convert ammonia into urea before expelling it from the body, which is much less toxic and does not require as much water, but requires energy

3. Birds, reptiles and insects convert ammonia into uric acid, which can be expelled in a solid form and hence requires very little water, but requires a lot of energy

Explain how the different processes of nitrogenous waste excretion in animals provide evolutionary insights

1. Life began in water, and movement to land birthed the urea and uric acid pathways, allowing animals to conserve water

2. Different reproductive characteristics also favour distinct nitrogenous waste removals; the water solubility of urea allows mammalian embryos to remove waste in their mother's blood, whereas the solid nature of uric acid allows waste from bird embryos to form harmless lumps inside of eggs

Describe the process of urine formation in vertebrate nephrons

1. Filtration: blood interacts with the tubules via the glomerulus (dense knot of capillaries), where water and other ions are filtered out of the blood into the Bowman's capsule

2. Reabsorption and secretion: most water and ions are absorbed back into the bloodstream from the renal tubules

3. Excretion: urea and waste ions are left behind in the tubules and increase in concentration as they head towards the collecting ducts (as water continues to leave), before being excreted as urine

Provide and explain an example of a difference in nephron structure across two different species

Freshwater fish nephrons have a larger glomerulus and a larger Bowman's capsule. This is because freshwater fish have a larger water content compared to their saltwater counterparts (due to greater osmotic concentration), and hence they need to filter out more water from their blood, producing more urine.

How do insects excrete nitrogenous waste in such dry environments?

1. The insect excretory system contains Malpighian tubules

2. The cells of the tubules actively transport uric acid, potassium ions and sodium ions from the extracellular fluid into the tubules

3. The high concentration of solutes in the tubules causes water to flow osmotically, flushing the tubule contents towards the hindgut

4. The epithelial cells of the hindgut and rectum actively transport sodium and potassium ions from the gut contents back into the extracellular fluid

5. The osmotic gradient generated pulls water out of the rectal contents, leaving behind a semisolid of uric acid and other wastes

Provide a mammalian adaptation to increase urine concentration and conserve water

The Loop of Henle: Functions as a counter-current multiplier, utilising energy to create an osmotic gradient that enables the reabsorption of water from the tubular fluid, so that urine can be concentrated.

Provide examples of abiotic environmental changes

1. Temperature

2. Humidity

3. Sunlight

Provide examples of biotic changes

1. Abundance of food

2. Competitors

3. Predators/Pathogens/Parasites

What is the difference between a signal and a cue?

Signals are any acts or structure that influences the behaviour of a receiver, and has evolved specifically for that effect, whereas cues are incidental sources of information that may influence the behaviour of a receiver but has not specifically evolved for that function