Notes.docx

TOPIC 1 -- EVOLUTION 1\. Describe the evidence supporting evolution and the raw ingredients for evolution to occur 2\. List the agents of evolutionary change and describe their impact on allele frequencies 3\. Apply the Hardy-Weinberg principle to demonstrate how allele frequencies can change ove...

TOPIC 1 -- EVOLUTION 1\. Describe the evidence supporting evolution and the raw ingredients for evolution to occur 2\. List the agents of evolutionary change and describe their impact on allele frequencies 3\. Apply the Hardy-Weinberg principle to demonstrate how allele frequencies can change over generational time 4\. Describe the reproductive barriers that lead to speciation, and consequences of hybridisation  5\. Explain how coevolution and arms races between predators and their pray impact survival 6\. Interpret information from different types of phylogenetic trees ----------------------- CONCEPT 1 - EVOLUTION ----------------------- - Carolus Linnaeus's classification system grouped biological entities based on similarities in their morphology. - Jean-Baptiste Lamarek's theory argued that living being could acquire characteristics within their lifetime & adapt to their environment (giraffes necks could go grow longer & traits passed to their offspring). - Nicholas Steno was one of the firsts to identify fossils as a source of hard evidence that could explain that the planet could change over time. - Mary Anning's fossils suggested that animal species could go extinct, which was controversial at the time. - Charles Darwin's evidence supported his idea that evolution was shaped by the process of natural selection. - Evolution -- cumulative change in the genetic composition of a population/species over time \- Individuals don't evolve, populations do. - Darwin's 3 Major Propositions: 1. Species are not immutable/fixed: populations show phenotypic variations & species can change over time 2. Descent with modification: Related species, which share a common ancestor, diverge from one another gradually over time. Eg. Bats use wings to fly, seals use flippers to swim & humans use their arms, the bones that make up these structures show similarities 3. Natural selection: differences in the phenotypes of individuals cause some to survive & reproduce more effectively. \- Ground finches in The Galapagos islands have different-sized beaks to crack open different-sized nuts - Speciation -- an evolutionary consequence of reproductive isolation. Eg. Darwin's finches on different islands. - Phylogenies can be produced using morphology, ie. a table of organism's traits - Node -- occurs when a lineage splits into 2, representing the most common recent ancestor of the species it groups - Branches -- can be terminal & lead to a taxonomic group, or they could be internal - Taxon -- the name of the entities that we are putting into it - Rooted tree includes the focal group of species being studied, as well as a more distant related outgroup species. -------------------------------------------- CONCEPT 2 -- AGENTS OF EVOLUTIONARY CHANGE -------------------------------------------- - Mutations can arise from misincorporation of the wrong nucleotide base - Mutations can also arise from DNA damage: \- [Spontaneous:] Replication errors, chemical reactions altering the structure & base-pairing properties of a DNA base \- [Non-spontaneous:] Chemical mutagen, some chemicals add groups to bases, radiation damage (UV) - Germline mutations affect gametes (eggs, sperm) and create the heritable genetic variation that is relevant for evolution. - Human mutation rate is about 10^-8^ mutations per nucleotide per generation or 50-70 individually. - Genetic Drift -- variation in the relative frequency of different genotypes & is more influential in small populations \- Stochastic/random changes (some pairs may produce more offspring or some multiple partners) allele frequency may change from 1 generation to the next, which is called genetic drift. \- Genetic drift removes variation, it does not add. - Population -- a group of individuals that have the potential to share genetic information & are all from the same species. \- Their geography defines population of asexually reproducing individuals - Gene pool -- total collection of alleles available in a population at any given time. - Natural selection -- a microevolutionary process that shapes the phenotypes of organisms to match their environment \- Natural selection is a *process* that acts on advantageous & deleterious mutations, whilst adaptation refers to a *trait* where only advantageous mutations contribute to it. - Macroevolution -- evolution *among* species spanning long periods of time, revealed through fossil records - Microevolution - evolution *within* species that can be observed directly acting upon natural populations. \- This process is influenced by the 'agents of change' - Non-random mating -- when individuals do not choose mates at random Eg. Alpha males in gorillas get more access to mating [- Assortative mating] shifts the gene pool as individuals more commonly mate with individuals with similar/dissimilar traits. \- When individuals preferentially mate with those of similar genotypes, homozygosity increases, whilst when individuals specifically mate with those of different genotypes, heterozygous allele combinations increase \- Eg. self-fertilization, height preference or inbreeding in royal families. \- Sexual selection is primarily about successful reproduction even when these traits reduce its chances of survival, seen in brightly coloured male bird species. Here, natural selection may act as non-adaptive. - Gene flow -- the spread of genetic variation across geographical area due to migration, hybridisation or gamete dispersal \- Gene flow counteracts the effects of population subdivision. Over time, gene flow increases genetic variation within subpopulations & can homogenise allele frequencies across the landscape. \- Individuals must be able to disperse, interbreed and produce viable offspring \- The [impact] of gene flow depends upon: 1. The genetic difference between populations, if the frequency of alleles is the same gene flow doesn't affect evolution 2. The level of migration, movement or hybridisation. - Recombination and independent assortment can create new combinations of alleles at different loci, creating new traits for natural selection to act upon. - When genes are located close together on the chromosome, recombination between genes occurs easier and evolution will speed up. ----------------------------------------- CONCEPT 3 -- THE HARDY-WEINBURG THEORUM ----------------------------------------- - Allele -- alternate forms of a DNA sequence - The Hardy-Weinburg Theorem: \- The B allele = occurs at the frequency *p* \- The b allele = occurs at the frequency *q*, where p + q = 1.0 \- Chance you sample alleles B x B + (B x b) + (b x B) + b x b, is given by: p^2^ + 2pq + q^2^ = 1.0 \- BB frequency = p^2^, Bb frequency = 2pq, bb frequency = q^2^ \- Frequency of the individual alleles B & b are given by: p = f~B/B~ + [\$\\frac{1}{2}\$]{.math.inline} f~B/b~ & q = f~b/b~ + + [\$\\frac{1}{2}\$]{.math.inline} f~B/b~ \- When given the frequency of 1 of the 2 alleles, you can interfere the frequencies of the 3 genotypes. \- Theorem shows allele frequencies will not change from 1 generation to the next \- The assumption is that the "agents of evolutionary change" are not acting. ie. no gene flow (migration), no mutation, infinite population size therefore no genetic drift, mating is random & equal fitness - Do Observed Frequencies Match Expected Frequencies? 1. Find allele frequencies p & q using population genotypes, using p = f~B/B~ + [\$\\frac{1}{2}\$]{.math.inline} f~B/b~ & q = f~b/b~ + + [\$\\frac{1}{2}\$]{.math.inline} f~B/b~ 2. Use theorem to find expected genotype frequencies BB, Bb & bb 3. Apply chi-squared test: χ^2^ = ∑ [\$\\frac{(O - E)\\hat{}2}{E}\$]{.math.inline} , O = observed, E = expected 4. Check if χ^2^ value is significant, if P value \< 0.05 null hypothesis is rejected (as its very unlikely to happen) & the alleles are not in Hardy-Weinburg equilibrium. \- For allelic data, degrees of freedom (d.f) = n-1 where n = no. of alleles - If observed genotype frequencies are too different, microevolution through migration, mutations, small population sizes, non-random mating and/or natural selection. ------------------------------------- CONCEPT 4 -- SPECIATION & VARIATION ------------------------------------- Speciation -- the evolutionary process by which new species arise through reproduction isolation (stopping gene flow), causing 1 evolutionary lineage to split into 2 or more lineages & are then unable to interbreed. - Requires genetic changes to accumulate & differ between populations through: new alleles becoming fixed and/or chromosomes being rearranged. - Allopatric Speciation: the ancestral population is divided by a physical barrier, preventing reproduction & gene flow. - Sympatric Speciation: ancestral populations are divided without physical or geographic barriers. \- It can be driven by the behaviour of other species, Eg. some flower colours can vary along closely related species since hummingbirds only pollinate red pendent flowers, whilst hawkmoths pollinate other species. \- Most common means is through [polyploidy], where 2 accidently unreduced diploid gametes combine & form a tetraploid individual (4 sets of chromosomes). Tetraploid & diploid individuals are reproductively isolated as there offspring are triploid & sterile, whilst tetraploid + tetraploid = tetraploid, same goes for diploid (common in plants due to self-fertilization). - Hybridisation -- interbreeding of individuals from genetically distinct populations which produce viable yet often sterile offspring \- [Dobzhansky Muller Model:] ancestral population divides into 2 distinct populations. A new allele arises at different loci in each lineage, neither of which result in any loss of reproductive compatibility by itself. However, if individuals from these separated lineages come back together, it's possible that new proteins encoded by the 2 new alleles won't be compatible with each other. \- If hybrid individuals are less fit, selection will favour parents that don't produce hybrid offspring \- Adaptive introgression: inheritance of beneficial variation from related species that accelerate adaption to, and survival in new environments. Occurs when hybrid organisms are fertile, Eg. homo sapiens + Neanderthals. An alternate explanation for Neanderthal introgression is the incomplete lineage sorting hypothesis. Poses that certain alleles were lost by chance or drift from humans in Africa, but the non-Africans & neanderthals retained these alleles. \- Mechanisms that prevent hybridization = prezygotic isolating mechanisms, those that reduce fitness of hybrid offspring = postzygotic isolating mechanisms. \- If reinforcement against hybridisation is occurring, then sympatric populations are expected to evolve more effective prezygotic reproductive barriers than do allopatric populations of the same species. - Prezygotic Isolation: barriers to reproduction *before* the union of the 2 gametes. \- [Geographical] isolation occurs when 2 closely related species prefer to live or mate in different habitats. \- [Mechanical] isolation occurs when there are differences in the size and shapes of reproductive organs. Eg pollinators \- [Behavioural] isolation occurs when individuals may reject, or fail to recognise, individuals of other species as potential mating partners, eg. different lacewings have a different calling pattern with different mating signals. \- [Mating time] differences eg. coral spawning times at sunrise or sunset. \- [Ecological] differences eg. sickled fish live in different ecological niches in their lake, some near the rocks and the deep bottom. \- [Gamete] isolation occurs when the sperm of 1 species may not attach to the eggs of another species because the eggs don't release the appropriate attractive chemicals or the sperm is unable to penetrate the egg because they're in compatible. - Postzygotic Isolation: barriers to reproduction *after* the union of the 2 gametes \- Fertilized egg/offspring is inviable \- Genetics, behaviour, physiology, or ecology of a species prevents hybrid zygotes from successfully developing & reproducing. - Reproductive barriers promote speciation along with the "agents of change" & enable speciation in allopathy or sympatry - The "Biological Species Concept" defines species as groups of actually or potentially interbreeding natural populations that produce *fertile* offspring. - Depending on the fitness of the hybrids, hybrid zones may either reinforce reproductive barriers between species, fuse species, or stabilise them. - Balancing selection maintains genetic variation (allele frequencies) in a population through the process: 1. Negative Frequency-Dependent Selection: \- Occurs when the fitness of a given phenotype depends on its frequency in the population. \- When a trait is rare, it can be more advantageous, and when it becomes common, its advantage might decrease. This creates a shifting balance where no single trait becomes overwhelmingly dominant. \- This system becomes cyclic & fails to reach an evolutionary state with consistent phenotypes. 2. Heterozygote Advantage: \- Occurs when heterozygous individuals have a fitness advantage over homozygous individuals \- A single allele is unlikely to perform well under all conditions (eg. hot & cold), so heterozygous individuals are likely to outperform homozygous individuals with only 1 of the 2 types of alleles. \- Eg. For sickle cell anaemia heterozygotes with a sickle-cell gene were most likely to survive as they offered protection against malaria which occurred in the same geographical region. - Relative fitness -- the success of the most advantageous genotype in a population relative to all other genotypes. \- Changes in numbers of offspring are responsible for the size change of a population, but only changes in the relative success of different phenotypes in a population will lead to changes in allele frequencies from 1 generation to the next. - Fitness -- success of an organism at surviving & reproducing. -------------------------------------- CONCEPT 5 -- COEVOLUTION & ARMS RACE -------------------------------------- - Sexual selection: 2 forms: Intersexual or Intrasexual \- Traits are costly to bear, so they are honest signals of mate quality (expected fitness) \- Traits will become exaggerated until balanced by natural selection \- Can occur [after mating:] 1\) Females can choose whether they use the sperm for fertilisation of the eggs. Eg. Female chickens can eject the sperm 2\) Often females mate with multiple males, meaning the sperm will compete to fertilise the eggs ('sperm competition') Eg. In damselflies, the males genitals have evolved to be able to remove any sperm present, so the last male can fertilise - Intersexual selection: non-random mating where one sex (often females) hold preferences for specific traits in mates \- Males spend a lot of energy growing their apparatus & showing it off sometimes unsuccessfully. \- Eg. Males in the African long-tailed widowbird have extremely long tail feathers as *ornaments* - Intrasexual selection: Individuals of the same sex (usually males) competing for access to mates \- Includes physical combat, display of strength and territorial battles \- Selects for the evolution & exaggeration of *armaments* (weapon traits) that are costly to bear or express. \- Contests are often ritualised, starting with display to avoid costly fights (signals such as roars) \- Eg. Male Southern elephant seals fight over territory where they maintain harems of females. - Sexual Conflict: Occurs when male & female have conflicts of interest over: whether mating occurs, female mating frequency (re-mating) & sperm use for fertilisation. \- Causes the evolution of traits that manipulate the other's sex's reproduction, both adaptions & counter-adaptions. \- Eg. Male pantry moths evolved giant spermatophores with mostly "cheap filler" sperm to make females believe they are full. So, females have evolved 'genetic teeth' to pierce spermatophores to reduce male manipulations of her mating frequency. - Coevolution -- process that occurs when an adaptation in one species leads to the evolution of a reciprocal adaptation in a species it interacts with. \- Eg. Pathogen evolves to enter the host, but the host then evolves to avoid the pathogen. \- Eg. The fastest cheetahs get the springbok so they can survive & reproduce, but the fastest springbok are selected for as they aren't eaten. - Red Queen Hypothesis: species must constantly adapt & evolve to survive while pitted against ever-evolving species \- "... it takes all the running you can do, to keep in the same place." - [How Prey Evolve to Avoid Predation:] \- Crypsis -- the ability of an animal to avoid visual detection by blending in with their environment. \- Aposematism -- a prey's visual cue to predators that it is hazardous or inedible Eg. Monarch butterflies \- Mullerian Mimicry - Harmful species with similar aposematic appearances share the cost of predator education. \- Batesian Mimicry -- Harmless species mimics a harmful one. Eg. King snakes copy banded pattern on venomous coral snakes - Antagonistic Interaction: are called 'arms races', where 1 species or individual benefits, whilst another is harmed. \- Types include predator-prey, plant-herbivore, host-parasite, brood parasitism & plant height. \- Eg. Monarch butterflies lay their eggs on milkweed species feeding on their nectar, beginning a competition: Milkweed got dense hairs on their leaves -\> Shave off their hairs first -\> Create sticky poisonous latex -\> Attacks leaf veins before eating leaves -\> Toxic chemical defence -\> Sequester chemicals for their own defences. - Mutualistic Interactions: where both species benefit from the interaction \- Types include plant-pollinator, cleaning, endosymbiotic & defensive \- Eg. cleaning fish remove the dead skin & parasites from the host whilst they get a good meal out of it. ------------------------------------ CONCEPT 6 -- EVOLUTIONARY GENOMICS ------------------------------------ - Phylogenies can be produced from a diverse character set: could look at morphological features themselves, compare pathways & the enzyme activities of these, the *protein* folds, amino acid sequences, RNA sequences or the *DNA sequences*. - For sets of DNA sequences, to build a tree we must ensure the columns represent homologous characters, which is done through a 'sequence alignment' (may shift rows over to create the fewest number of changes). - Nucleic acid sequences are useful as they occur in all biological entities, have homologous sequences, large amounts of data & have a consistent mutation rate. - Different Types of Trees  - A Molecular Clock: \- The amino acid divergence of proteins against time of all different species, was found have the data fall on a straight line. \- Trend is so strong we can use sequence divergence as an approximation for years. - Genetic approaches have allowed us to identify the genes & the mutations that underlie adaptive phenotypes - Mutations are often complex; duplication of sequences & transposable elements (virus like elements moving around genomes) - [Population structure] arises when a demographic process produces systematic differences in allele frequencies between a subset of a larger population, typically arises from a factor that causes non-random mating \- It can be said individuals in group 1 look alike, same is said for group 2 \- Group 1 & 2 may in interpreted as having divergent evolutional histories \- Cluster of organise & blue on RHS only differ in the groups by the frequency by w by which both groups are, this is more typical.  - Apart from Africa, Indigenous Australians have the highest proportion of variants that are 'private' to a continent. TOPIC 2 -- PHYSIOLOGY 1. Compare and contrast the features of different gas exchange systems across plants, animals and fungi. 2. Describe the diversity in excretion/waste elimination strategies across the tree of life. 3. Explain the key mechanisms that enable organisms to sense and respond to their environment. 4. Explain how animals maintain constant temperatures through physiological or behavioural responses. 5. Describe the evolution and diversity of the different reproductive strategies present across the tree of life. 6. Compare and contrast the features of immunity that enable plants, animals and fungi to respond to threats within their environment. ------------------------------------------------- CONCEPT 7 -- RESPIRATION & GAS EXCHANGE SYSTEMS ------------------------------------------------- - To enhance features of gas exchange surfaces: Large SA:V ratio, thin membranes, partially permeable, movement of fluids/gas across these surfaces in both internal & external environment to maintain a diffusion gradient. Plants - - Different plants exhibit different shapes of their stomata & guard cells, which changes the degree to which they can open - Some have kidney-shaped stomata formed on the leaf epidermis, whilst others have dumbbell shaped stomata with neighbouring subsidiary cells -- these are collectively termed a stomatal complex - Don't have a specialised network for gas transport, so each part of the plant takes care of its own gas exchange needs - Stomata can often be found on leaves (highest proportion of stomata), stems, petals & roots of plants \- Roots can extract O2 from air pockets within the soil via root hairs which help increase SA to exchange gas, water & nutrients - Cells are loosely packed with an interconnecting system of airspaces, where gases can diffuse 1000X faster than through water \- In stems, these airspaces form aerenchyma which help exchange gases between stems & roots \- Aerenchyma is the space between the cells, which form when cells separate or collapse  - For thick stems the only living cells are organised in thin layers just beneath the bark - In woody stems & shoots there are no stomata, but there are small pores called lenticels \- Lenticels allow gases in & out and interact directly with the living tissue - Wetland Plants: gas exchange is similar to using a snorkel \- Air enters into common reeds from short broken stems/dead plants that are all connect via underwater structures -- rizomes \- CO2 diffuses out through other taller broken stems \- O2 moves through the aerenchyma driven by changes in air pressure due to the different size of the broken stems of plants. Fungi -- can be both unicellular or multicellular - Rely on diffusion through their cell or body walls, lacking specialised gas exchange structures - Gas exchange requirements are quite low (they're slow growing or dormant) - Majority of gas exchange in multicellular fungi takes place via the large branching network of mycelium \- Mycelium possesses microscopic hyphae that extend into small crevices in the soil to interact with small air pockets - Can produce fruiting bodies with porous & thin body walls that extend above the substrate into the air - In larger or more active species, specialised gas exchange structures have evolved based on the habitat & lifestyle of the animal - 2 Main Processes to Ensure Efficient Gas Exchange 1. Ventilation: gasses are moved across the gas exchange surface, either via body movements or movements of the respiratory structure itself = optimal pressure gradient for diffusion 2. Circulation: gases are moved to & from the exchange surface & the body tissues \- Can occur via dissolution into a circulatory fluid (like blood) or directly via a network of branching tubes - To ensure respiratory surfaces stay moist, terrestrial animals have internal gas exchange structures Insects -- - Use a network of air-filled tubes called trachea, whose system allows direct O2 delivery to tissues & cells - Air enters via spiracles located along the sides of the thorax & abdomen through tracheae -\> tracheole -\> fine air capillaries - Can close their spiracles to prevent water loss & contract their abdomen, which is a form of ventilation that sucks more air & O2 Terrestrial Animals -- highly vascularized lungs (mammals) - Air through nose/mouth -\> trachea -\> branching into the bronchi -\> bronchioles (depending on the animals oxygen requirements) which end in alveoli - Lungs walls are thin & are surrounded by many capillaries providing a large SA for gas exchange & are kept moist by surfactants \- Surfactants -- special molecules with a hydrophilic & hydrophobic end secreted by pneumocyte cells within the lung \- Attractive forces working on H2O molecules at the surface pull from the sides & below, this imbalance creating surface tension \- To inflate the lungs, enough force is needed to overcome the elasticity of the lung tissue & surface tension of the alveoli \- These lung surfactants reduce the surface tension of the liquid reducing the work/pressure necessary to inflate the lungs. [Birds:] need high rates of gas exchange since their O2 requirements at rest are higher than that of all other vertebrates \- System involves a unidirectional flow of air \- Mammalian lungs are never completely empty after exhalation (dead space), there's always some lung volume not ventilated with fresh air. In contrast, birds have very little dead space, and the fresh incoming air is not mixed with stale air. \- Lungs don't move but are ventilated by air sacs that pump air to & from the lungs in specific orders \- Fresh air passes over the gas exchange surfaces during both inhalation & exhalation resulting in a constant supply Aquatic Animals -- fishes gills - Gills are made of many filaments covered in lamellae to increase SA & thin tissues to minimise path length of O~2~ & CO~2~ - As water flows over the surfaces, O2 diffuses into the blood within the gill capillaries (reverse goes for CO2 into the water) - They employ a counter-current exchange mechanism where water & blood flow in opposite directions - The counter-current flow maximises O~2~ transfer from water to blood because all points along the exchange surface there is a P~O2~ gradients between water & blood that never reaches an equilibrium like it does halfway through a concurrent flow. ----------------------------------------------------------- CONCEPT 8 -- NUTRITION, DIGESTION & EXCRETION ADAPTATIONS ----------------------------------------------------------- Adaptation of Autotrophs -- capable of producing the majority of the nutrients required for cellular metabolism themselves - Capture radiant energy from the sun & with chloroplasts fix it into organic compounds using CO2 & water into glucose. - In others, energy from transforming carbon into food can come from the oxidation of inorganic nutrients Eg. by chemosynthesis - Chemosynthesis: by bacteria or archaea in ecosystems that lack sunlight & have high conc. of particular inorganic compounds \- Such inorganic compounds could be the H~2~S gas that is released at deep sea hydrothermal vents \- These organisms live as symbionts in other heterotrophic organisms, such as within giant tube worms \- They convert dissolved CO2, O2 & H~2~S into carbohydrates, which can then be used by the bacteria themselves or by their host \- H~2~S is primarily oxidised to form sulphite, thiosulphate & elemental sulphur & ATP which is used to convert CO2 into glucose \- The major pathways for C fixation are the *Calvin Cycle* & the *reductive carboxylic acid cycle* \- 18H~2~S + 6CO~2~ + 3O~2~ C~6~H~12~O~6~ + 12H~2~O + 18S Adaptation of Heterotrophs -- organisms that must obtain the majority of their nutrients from other organisms - They're referred to as consumers or decomposers & can feed upon autotrophic/heterotrophic organisms & living/dead matter - Primarily relate to the *source & collection* of food, which is related to how mobile they are - *Mechanism* by which they break down the food item into soluble & transportable compounds (mechanical/chemical digestion) - The tissues & transport systems associated with the *absorption* & its stimulation of key nutrients into the body. - While many plants & fungi are autotrophic, some rely on organic matter from their surroundings, as they can't move far, they posses adaptations primarily for chemical digestion. Eg. to break down dead/decaying matter as seen in many fungi \- Eg. To invade the vascular tissue of other plants (seen in parasitic plants), enabling uptake of nutrients & maybe the transfer of RNA & pathogens from parasite to host \- Eg. Break down trapped living organisms, such as in carnivorous plants which produce chemical or physical signs to attract pray - Animals most notably have modified mouth parts such as teeth of vertebrates, or different mouth parts of insects used to siphon or suck liquids or capture & mechanically process prey - Modification of the limbs for manipulating or capturing prey (Eg. different claws) Acquiring Nutrients in Plants: - Rhizobacteria in the soil receive nutrition from plant roots, while they may produce antibiotics to protect the plant, absorb unwanted chemicals or help the plant get essential nutrients - Plants can't use atmospheric nitrogen, so during 'nitrogen fixation', prokaryotes convert it to ammonium then to nitrate both of which can be taken up & used by the plant - Fungi (Mycorrhizae) are in a mutually beneficial relationship as they receive nutrition from the plant, & in return the fungi can access nutrients otherwise unavailable to the plant by expanding the root surface area or getting into tiny pore in the soil, act as a physical barrier to pathogens or produce antibiotics to protect it. - Carnivorous plants (in acidic & nutrient-deficient environments) obtain extra N by catching animals, digesting their proteins & absorbing their amino acid Excretion of Waste in Plants: - They recycle majority of waste as a product of photosynthesis = reactants of cellular respiration & vice versa, yet the balance of they processes aren't always even & some excess gasses & water do need to be removed to maintain homeostasis - Metabolic waste is removed via leaf stomata through transpiration. Evaporation of water vapor generates pressure in the leaves which draws water through the xylem & facilitates absorption of water via the roots - In some plants, permanently open pores called lenticels also allow removal of a very small proportion of unwanted water/gasses - Plants generate nitrogenous waste products by protein metabolism, which can be excreted or reused for protein synthesis - [Shedding:] Can also store unwanted byproducts in the vacuole of the cell often in the form of amino acids, mineral salts & water \- These wastes build up over time in tissues that can be shed from the plant as it ages, such as in the fruit, leaves or bark. - Guttation: occurs when root pressure & its absorption of water exceeds transpiration, forcing xylem sap through secretory cells in the leaf epidermis called hydathodes. Acquiring & Transporting Nutrients in Animals - [Fungi Digestion:] small molecules accumulate in a watery film surrounding the hyphae or yeast & simply diffuse through \- Macromolecules undergo 'preliminary digestion' which involves the release of enzymes in pus/exudate from the hyphae or yeast, facilitating extra-cellular breakdown & diffusion of products into the cell or body. - Circulatory System - where digested compounds are transported around the body to where they are needed - Digestive tract -- where food is broken down into constituent components within this specialised organ system. \- Simple guts are found in sponges where H~2~O flows through its body through water channels & each cell captures food particles - Also in Cnidarians & platyhelminths where there's a singular opening to the gut or gastrovascular cavity lined with cells that produce digestive enzymes that absorb nutrients. \- It's divided into 3 sections: foregut, midgut & hindgut \- [Foregut:] the intake & storage of food as well as the initial stages of chemical & mechanical digestion \- [Midgut] & [Hindgut:] for chemical digestion & absorption of nutrients prior to defecation of waste products \- Herbivores: Mouth parts for grinding, cutting & shredding have evolved to break down low energy & difficult to digest food \- Mechanical digestion continues in the stomach or crop which is very muscular so that food can be squeezed & churned \- This region of the foregut also contains acids & digestive enzymes \- Foregut fermenters: In ruminants (cows) the stomach is split into 4 sections, the first 2 the rumen & reticulum, are packed ggiwith endosymbiotic microorganisms that break down cellulose by fermentation. \- The contents of the rumen are periodically regurgitated into the mouth for rechewing before going to the other regions. \- Hindgut fermenters: have a simple stomach but rely on very long hindguts where caecum posses an array of microbes \- Herbivores rely on symbiotic bacteria, protozoa & fungi within their digestive tracts to break down cellulose  \- Carnivores: rely less on mechanical digestion & more on chemical digestion which starts in the mouth via salivary enzymes \- Stomach & foregut are highly acidic (digest proteins), while midgut secretes bile to digest lipids \- Digestive tracts are shorter & less complex than herbivores, as there's little need for storage of food within it. - Increase SA:V for absorption through inward folding of parts of the gut (earthworms), additional tissue within the gut (spiral valve of sharks), or villi that posses tubes or folds called microvilli (from insects to humans) Excretion of Waste in Animals: - Aquatic Environments: ammonia is simply passed across the body wall \- Many excrete nitrogenous waste & other ions across their gills, but in invertebrates that main route for excretion is via kidneys \- Functional unit of the kidney is the nephron, which is made up of a blood vessel & tubule component \- Urine formation involves 3 main processes: 1[) Filtration:] blood interacts with the tubules via the *glomerulus*, & water + ions are filtered into *Bowman's capsule* 2\) [Reabsorption & secretion:] blood flows into another network of capillaries that interact with renal tubule & reabsorb & iiiisecrete solutes. This process increases the ionic concentration as it flows towards the collecting ducts of the kidneys 3\) [Excretion] - Length of the structures in the nephron varies based on the environment Eg. freshwater fish have a larger filtration section to produce dilute urine in large volumes since the osmotic concentration of their body is higher than the surrounding water - Insects: excrete nitrogenous waste with little loss of water & can therefore live in some of the dryest habitats on earth \- Excretory system contains several 'malpighian tubules' that open into the gut between the midgut & hindgut \- Cells of the tubules transport uric acid, K+, Na+ from the extracellular fluid into the tubules \- This high conc. solutes causes water to flow osmotically flushing the tubule contents to the gut \- Osmotic gradients pulls water out of the rectal contents, & remaining in the rectum is uric acid + other wastes to be excreted - Terrestrial Environments: kidney is main organ for waste excretion, yet the structure of the nephron differs based on the class \- Mammals have adapted the "Loop of Henle" which is a longer proximal tubule that extends into the medulla region \- In arid environments where water conservation is crucial, the kidney is particularly efficient & makes the highest urine conc - The loop creates a gradient of increasing osmolarity (saltiness) in the kidney's medulla, allowing the kidneys to reabsorb more iiwater from the filtrate as it moves through the collecting ducts ------------------------------ CONCEPT 9 -- SENSORY SYSTEMS ------------------------------ - Extent to which [abiotic conditions] changes is very different for temperature, humidity & sunlight - Spatial changes in the [biotic environment] are crucial to detect, such as the abundance of food, presence of competitors or threats from predation and pathogens, as well as the capacity to find suitable reproductive partners - Information about changes in the environment are provided by the presence or absence of certain signals & cues - Signals & cues have no 'intrinsic' (belonging naturally) meaning they just provide information - Signals & cues but be readily & reliable (repeatably provides the same information) discernible from background noise \- To distinguish valuable cues, they must use different sensory modalities which depend on its location & lifestyle \- Organisms can use chemical, electrical, mechanical, photic, magnetic or auditory modalities to discern cues \- Each organisms has a range within each of its sensory modalities that it can perceive cues Eg. Hearing ranges or animals - Signals -- any act or structure that influences the behaviour of other organisms (receivers), and which evolved specifically because of that affect they have on their intended receivers \- Change in its purpose occurred in the bioluminescence of beetles, first evolved as a warning signal but is now a mating signal - Cues -- an incidental source of information that may influence the behaviour of a receiver, despite not having evolved under selection for that function. Can come from abiotic features, or from another organisms. \- Wallabies were less likely to forage in areas where the faeces from dogs, who had eaten other macropods, were found - Chemoreceptors (chemical sensitive) -- activated through physical interaction with molecules through a lock & key mechanisms \- [Direct Activation:] molecule attaches to a receptor & this interaction directly opens a channel in the cell membrane \- [Indirect Activation:] interaction causes activation of another protein in the cell that carries the signal along opening a different iiprotein channel through which ions pas - Thermoreceptors (temperature sensitive) -- change shape in response to changes in temperature enabling the passage of ions - Mechanoreceptors (motion sensitive) -- activated through stretching or movement, opening the channels allowing ions through - Photoreceptors (light wavelengths) -- when a photo bumps into a photoreceptor protein, the protein absorbs its energy and temporarily changes shape Plants - - Photoreceptors contain a protein component & a light-absorbing pigment (chromophore) - Each specific chromophore absorbs light of a particular wavelength causing a structural change, triggering a signalling cascade - This can lead to gene expression affecting plants\' growth & morphology \- Eg. 2 forms of phytochrome receptors, inactive (P~r~) absorbs redlight active (P~fr~) absorbs far-red light, the ratio of which reaches an equilibrium in daylight. So, plants in the shade sense this ratio of red to far-red light & adjust its growth - [Biological clocks] sense environmental variations, such as changing light levels, allowing plants to follow daily behavioural cycles \- Also allows plants to respond to seasonal changes through the phytochrome system - Photochrome System: \- Phytochromes measure the day length ([photoperiod]) & regulate photoperiodism (biological responses to the photoperiod) \- They're synthesised in the dark as the inactive P~r~ form in the cytoplasm, during the day it absorbs red-light & converts it to Pfr \- P~fr~ activates molecules or translocated to the nucleus & regulates gene expression \- At night, P~fr~ levels decline due to the slow darkness reversion into P~r~ or the destruction of P~fr~ by enzymes \- Long nights = no P~fr~, short nights (during the summer) = considerable amounts of P~fr~ remain at sunrise - In roots, the root cap contains gravity-sensing cells (astrocytes), which within them contain dense, organelles called amyloplasts, which settle downward in response to gravity - Thigmotropism -- the direction growth exhibited by plants in response to touch [- Negative Thigmotropism -] roots grow away from objects they touch, allowing them to follow the path of least resistance [- Positive Thigmotropism --] threadlike tendrils in climbing plants grow towards objects they touch, sometimes rapidly coiling - Tendrils\' contact with a stimulus induces the contraction of cells at the contact side & the elongation of cells at the non-contact side, this differential growth eventually causes tendrils to twine around the object, securing it Animals - - Sensory transduction begins with a receptor protein that opens or closes ion channels in response to a specific stimulus which alters the receptor cell's membrane potential - All sensory systems process information in the form of action potentials generated by sensory receptors, but the sensations we perceive differ because the mssgs from different kinds of sensory cells arrive at different places in the CNS - Intensity of a stimulus depends on the amount in the optimal range, the number of receptors activated at a given time, or the rate of action potentials by the receptors Chemoreceptors - Olfaction: sense of smell \- Olfactory receptors are neurons in a layer of epithelial tissue in the upper region of the nasal cavity \- The dendrites of these neurons project as olfactory cilia on the surface of the nasal epithelium, and there axons extend to bulb \- A complex odorant can activate a unique combo of nerve clusters in the bulb known as glomeruli \- [Olfactory sensitivity --] discrimination of many more odorants than there are olfactory receptors  - Pheromones -- chemical signal used for communication among individuals in the same species \- Triggers behavioural responses such as attracting mates, alarm signals, mark food trails or define territories \- Sensory organs for detection differ in species, Eg. insects use antennae to seek mates, mammals use the olfactory system - Gustation: sense of taste \- clusters of chemoreceptors (taste buds) have microvilli on their tip and these cells generate action potentials & release neurotransmitters at their bases, where they form synapses with sensory neurons that convey the signals to the CNS - Detection of light can impact mass movements of animals, as seen in the vertical migration of different animals in the oceans \- Heterotrophs move from deeper waters during the day, returning to the surface at night, using light receptors - In vertebrates, entrainment of the circadian clocks in the body is controlled by the connection between photoreceptors in the eye & special regions in the brain, called the suprachiasmatic nucleus (SCN), which sit in the hypothalamus deep within the brain \- SCN receives info from the eyes via the retinohypothalamic nerve tract which stimulates the release of neurotransmitters - Somatosensory System -- components of the central & peripheral nervous system that process touch, pain, pressure & tem \- [Receptor level:] stimulus excites a sensory receptor, & its converted into an electrical signal, generating a graded potential \- [Circuit Level:] impulse reaches the CNS, the majority of which reach the primary somatosensory area \- [Perceptual Level:] interpretation of the sensory input by the CNS & only the impulses processed in the cerebral cortex are consciously perceived. --------------------------------------------- CONCEPT 10 -- HOMEOSTASIS: THERMOREGULATION --------------------------------------------- - [Temperature Response Curve: ] \- Rate of reaction tends to rise with increasing temp to an optimal level & then fall again \- Q~10~ = R~T~ / R~T\ --\ 10~ unitless variable which denotes the rate of change over a 10 degree change in temperature \- Q~10~ = 1 the reaction is not temperature sensitive (straight line), Q~10~ = 2 indicates a doubling in reaction by each increase of 10  - To ensure essential processes occur at optimal rates for survival organisms can: \- Acclimate/adapt to their surroundings, shifting the optimal rate of reactions into the range of temps to which they're exposed \- Have a broad range of temperatures at which important biological reactions are optimized \- These strategies are effective in organisms that are sedentary or less mobile like plants & fungi, or unicellular organisms \- In larger & more mobile species, thermoregulation occurs via physiological & behaviour means Thermoregulation -- control of internal body temp, either by physiological or behavioural means - In roundworms thermoreceptors synapse to interneurons that connect to motor neutrons eliciting a thermotactic response \- [Thermotactic response] is a motor response to temperature enabling them to move to more suitable microclimates. - In more complex taxa, like vertebrates, peripheral NS detect changes via thermoreceptors, sending info through cns -\> hypothalamus -\> physiological responses (Eg. vasodilation/vasoconstriction or activation of skeletal muscles for shivering) - Physiological: \- Endotherms -- produce the majority of their body heat themselves from internal metabolic processes \- Ectotherms -- rely on gaining heat for thermoregulation from external sources, such as the sun \- Homeotherms -- maintain a stable body temperature \- Heterotherms -- body temperature that fluctuates, either on a regular basis or under specific conditions or life history stages - Homeothermic ectoderm often in environments with stable temperatures, meaning they often cant survive outside a very narrow range Eg. marine animals in water of a very specific temperature - Heterothermic endotherms using hibernation to survive the cold by dropping their body temperature to the surroundings. \- Different from ectoderm since they use endogenous heat to warm up from hibernation & then maintain stable body temp - Behavioural: adjust their activity and/or move to different microclimates within their habitat Eg. ectotherms rely on this Metabolism - - [Ectotherms:] simplest as physiological variables, such as metabolism, increase with environmental temperature until optimal \- Thermal tolerance is bounded by critical thermal min/max (CT~min~/CT~max~)  - [Endotherms:] can increase or decrease metabolic heat production in response to their external environment \- Thermoneutral zone -- range where the cost of maintaining optimal body temp is minimized \- Below or above this range means metabolic heat production has to increase to compensate \- Mechanisms for heat loss, like panting & sweating require energy - Rate at which an animal exchanges heat is defined by its thermal conductance \- Thermal conductance is determined by the size, shape, & thickness of any layers of insulation in an animal (fur, scales or fat) \- Greater thermal conductance = steeper relationship between metabolism & temperature & vice versa (low = shallow) \- In endotherms, greater thermal conductance in small animals, shrinks the range of the thermoneutral zone, compared to larger animals with lower thermoconductance having a wider thermoneutral zone - Both ecto & endoderm's influence their body temp by altering 4 avenues of heat exchange between their body & environment \- Radiation: heat moves from warmer objects to cooler ones via the exchange of IR \- Convection: heat exchanges with a surrounding medium such as air or water that flows over a surface (the wind-chill factor) \- Conduction: heat flows directly between 2 objects at different temps when they come in contact (Eg. icepack on an ankle) \- Evaporation: heat is transferred away from a surface when water evaporates on that surface (the effect of sweating) since the heat capacity of water is much greater than that of air - Heat is mostly moved around the internal environment by blood flow. Blood flow to the skin enables internal heat to be lost to the environment, thus bringing the body temperature back to normal (thus cold = constriction of blood vessels) \- Mammals with fur have specialised blood vessels for transporting heat to hairless skin surfaces - Warm blood flowing out the paw of a wolf parallels the flow of the cooler blood returning to the body core to retain heat - Comparison of metabolic rate in endotherms is most comparable when measured in the thermoneutral zone \- This region where heat loss/gain are equal is called basal metabolic rate (BMR) \- Must be collected from animals that are resting, post-absorptive (not digesting or feeding) or non-reproductive - Equivalent value for ectotherms is termed standard metabolic (SMR), under previous conditions + same temperature - Metabolic rate is primarily related to body mass, not other ecological factors \- Across all endoderm's, BMR per gram of tissue increases as animals get smaller, many hypothesis for why this is \- Endotherms in cold environments have evolved smaller SA:V ratios to maintain heat through rounder body shapes --------------------------- CONCEPT 11 - REPRODUCTION --------------------------- - Evolution: first 3 billion years of solely asexual reproduction, then 1 billion years of sexual reproduction as well - Unlike asexual reproduction, sexual reproduction is only found in the 4 eukaryotic kingdoms: Protista, fungi, plantae & animalia - Dioecious -- individual has either male or female reproductive systems - Monoecious -- individual can posses both male & female reproductive systems aka. Hermaphrodites - Oviparous -- embryo develops within an externally laid egg - Viviparous -- embryo develops internally within the parent Asexual Reproduction: - Fission -- parent cell or organism separates itself into equally sized daughter cells or organisms \- Found occur all kingdoms & domains but most common in Bacteria, Archaea & Protista \- [Binary fission] occur when a parent produces 2 equally sized offspring, involving the initial enlargement of the parent cell and a iiduplication of the nucleus before division. \- [Multiple fission] results in numerous offspring which is particularly fast & initially occurs via the division of the nucleus into iimany parts, after which the cytoplasm forms around these nuclei & the organism separates. - Budding -- occurs via a small outgrowth that forms on the parent cell or organism & tends to form in a specific location \- This then breaks off to form a new smaller daughter cell (2 unequal parts distinguish it from fission) - Fragmentation -- parent organism breaks into fragments, each capable of growing independently into a new organism - Vegetative Propagation -- only occurs in plants in which detached root or stem fragments can develop into an entire new plant \- Since they're sedentary, many forms involve the movement of offspring away from the parent plant to reduce competition \- In runners or suckers an extension of the root system moves away, and it can be cut from the parent & survive on its own. \- Artificial methods includes [grafting] -- combines upper & lower portion of plants to get favourable traits from different varieties \- Eg. a scion (upper part) with large fruit may be grafted onto a disease-resistance rootstock (lower part) - Parthenogenesis -- in multicellular plants & animals via the development of offspring from unfertilised or self-fertilized gametes \- Most commonly an egg cell \- Often occurs in species also capable of sexual reproduction, so they can take advantage of both reproductive strategies - Can be part of the mechanism that determines sex, such as haploid males in honeybees, & most ants & wasps Sexual Reproduction -- - Occurs via meiosis where diploid parent cells divide to form haploid daughter cells - Fertilization occurs when 2 daughter cells combine to form a diploid zygote - Some organisms are primarily diploid (most animals), with only the gametes being haploid - [Alteration of generations:] Plants, algae & protists have a life cycle that alternates between 2 mature diploid & haploid phases \- In plants meiosis produces spores which then develop into an adult by themselves, after they germinate they undergo mitosis forming a multicellular but haploid gametophyte that then produces gametes \- The gametes from 2 different gametophyte parents then fuse -\> diploid zygote -\> grows into the diploid sporophyte - Angiosperms (flowering plants) usually have [carpels] for female sex organs that create & store eggs & [stamens] which are male sex organs that produce and release sperm. \- To prevent inbreeding male & female gametophytes are separated & many plants are genetically self-incompatible - Eg. in a sexually reproducing fern: - [Primarily Haploid:] most fungi \- Individuals aren't males or females but have many different mating types \- In sexually reproducing individuals, any 2 of these types can mate with one another \- When they mate, they fuse their bodies to become one which is called plasmogamy -- the cytoplasm of 2 haploids fuse \- This phase can last for some time before genetic sex/fertilisation occurs and the nuclei fuse to form a diploid individual \- Karyogamy -- fusing of nuclei in dikaryotic fungi \- After this, meiosis occurs, and haploid spores are released into the environment which form mycelium that begins the cycle  - Thought to have evolved from a monoecious ancestor where meiosis produces haploid gametes of both sexes (F + M) \- Has benefits of both asexual & sexual reduction, such as genetic variation & 100% of the population able to produce offspring \- Though to have occurred by gradual increase in investment in one or other of the sex roles, seen in the production of gametes \- Isogamy - each parent has an equal investment in the production of gametes & the gametes & therefore the same size \- Anisogamy - parental investment is different, & one parent invests more energy into the production of large gametes - Simultaneous hermaphrodites -- individuals that produce both eggs & sperm at the same time Eg. earthworms - Sequential hermaphrodites -- vertebrates & invertebrates & are individuals who can function as either male or female at different stages in their lives. Change between sex is determined by conditions, social structure or age \- Beneficial in conditions where the likelihood of finding a mate is very low, or the reproductive season is very short ------------------------------ CONCEPT 12 -- IMMUNE SYSTEMS ------------------------------ - Immune system is thought to have originated alongside multicellularity, so in animals plants & some fungi in particular - Origin: evolved to protect against invaders, or an alternative hypothesis is that it emerged to manage the microbiota 1\) Recognition Phase: organism recognizes the pathogen as foreign because it can discriminate between self & non-self cells - Specific "*pattern recognition receptors*" are located at the surface of cells & can detect general features of groups of organisms - Micro-organism/ Pathogens are terms *Pathogen/Microbe associated molecular patterns* (MAMPs or PAMPs) (don't have to cause disease) - These patterns are specific to the micro-organism, so they're not present in the host body cells, so they're considered non-self - Major Histocompatibility complex (MHC) proteins are used to display antigens on the surface of self cells, so that the antigen can be detected by the T cells of the immune system. 2\) Activation Phase: mobilisation of cells & molecules to fight an invader - Binding of MAMPs to pattern recognition receptors activates the initial immune response within a cell such as: \- The secretion of antimicrobial peptides ([defensins]) which break apart the cell membrane of the invader \- Production of cytokines which are released & recognised by specific surface receptors on other cells, primarily immune system cells, which can activate additional responses of the immune system 3\) Effector Phase: mobilised cells and or molecules destroy the invading micro-organism - In most plants & fungi, this stage results in the death of the affected cell & pathogen, which is known as regulated cell death Innate Response -- or nonspecific defence, mechanisms that provide the 1^st^ line of defence (acute defence) - Typically act rapidly & recognizes broad classes of organisms and molecules, such as viruses, bacteria, fungi ect. - Physical Barriers: 1^st^ Line \- Thick skin: plants have thick waxy cuticles and many animals have a cuticle layer above their epidermis, which can be made of: layers of chitin (seen in insects) or keratin as in the scales, fur & feathers of most vertebrates \- Eyes have eyelids which can be made up of extra flaps of skin or as an additional membrane like the nictitating membrane \- Presence of mucous: slippery secretion with antimicrobial properties or trap pathogens for removal by the beating of cilia. \- In animals, the respiratory tracks (lungs) are protected by cilia & the production mucous to move pathogens out via coughing \- Presence of lysosomes: enzymes that are secreted into mucous and attacks the cell walls of many bacteria, bursting them \- Presence of defensins: made my mucous membranes, are toxic to a range of pathogens & insert themselves into the cell membrane of these organisms & make the membranes permeable, thus killing them. \- Presence of extreme conditions: such as gastric juices in the stomach \- Presence of normal flora compete with pathogens for space & nutrients. - Cellular Response: 2^nd^ Line involves recognition of pathogen or damage \- White blood cells (neutrophils, monocyte-derived cells, & mast cells) express receptors that allow them to recognize pathogens \- In insects & many invertebrates, mast cells release cytokines, which attract other phagocyte cells which will engulf pathogen. Pathogen is thus isolated from the rest of the body, slowing the spread of infection Inflammation: Isolates the damaged area to stop the spread of the damage, recruits cells to the damage & promotes healing - In vertebrates, the response is led by mast cells which secrete cytokines to activate other immune cells & promote increase of blood flow to the infected area as well as increase the permeability of the blood vessel & generate a clotting response - Plant Innate Defences: no acquired immunity, only PRR, physical barriers, chemical defences & regulated cell death \- Plants can recognise the protein flagellum on bacteria for example, triggering a signalling cascade leading to a response such as the closure of stomata, the production of antimicrobial chemicals, & the strengthening of the cell wall \- Some pathogens inject *effectors* that stop the signalling cascade, which some plants have evolved resistant effector molecules \- To attack herbivores they may use chemical that disturb the digestive system or harm their skin or attract a parasite Acquired/ Adaptive Immunity: aimed at specific pathogens and are activated by cells in the innate system - Targeted (recognises specific antigen for a particular pathogen) but slower response (long-term defence) - Differs from innate as it has T & B cells & develops an immunological memory - Humeral response -- antibodies defend against infection in the blood & lymph \- B cell is activated by antigen binding to its receptor, and after stimulation by a T~H~ cell due to its release of cytokines, it divides into clones of plasma cells (effector cells), and a small number of memory B cells \- Which secrete millions of antibodies that activate several defence mechanisms such as: \- Antibodies -- proteins that bind to certain substances labelled as foreign, the specific molecules that bind to them as antigens 1\) Neutralisation: antibodies bind to antigens on the surface of a pathogen inactivating or neutralizing as it cant infect a host cell 2\) Opsonization: or tag pathogens, for engulfment & destruction by phagocytes 3\) Complement Activation: activates a complex of proteins that further enhances the destruction - Cell-mediated response -- cytotoxic lymphocytes defend against infection \- 1^st^ line of defence are white blood cells called macrophages which digest the pathogen which contain antigens on their surface \- Phagolysosome fragments the antigens and transports them to the surface \- Other proteins then embed the antigen fragments for presentation on the surface of the antigen presenting cell (APC) \- The complex can now be detected by T lymphocytes or T cells another white blood cell that multiplies rapidly by mitosis \- [Helper T cell:] secrete chemicals to subulate the growth & differentiation of [Cytotoxic T cells] which kill cell by apaptosis \- [Memory T cell:] remain after just in case the same pathogen is re-encountered \- [Suppressor T cells:] inhibit the immune system once the infection is controlled to prevent further destruction of host tissue  TOPIC 3 -- ECOLOGY 1. Explain different life history strategies and their inherent trade-offs 2. Summarise how scientists study and estimate populations 3. Explain different population models and how they are affected by stochasticity 4. Describe the key processes that drive dynamic populations 5\. Explain ecological processes, symbiosis, parasitism, mutualism, using examples 6\. Apply ecological concepts to examples of biological control and restoration --------------------------------------- CONCEPT 13 -- LIFE HISTORY STRATEGIES --------------------------------------- - Life History -- patterns of survival & reproductive events for a species, there's 3 categories: [1) Number of Reproductive Events:] - Semelparous (semi as in "single") -- individuals breed once in their life \- Death after reproduction is a strategies that must all rescourses into maximising reproduction Eg. salmon - Iteroparous (iter from iterate = "repeat") -- individuals (potentially) breed mutliple times in their life \- Multiple reproductive cycles Eg. most birds & mammals [2) Duration of a Generation:] - Several generations per year - Annuals -- 1 generation per year or season \- In strongly seasonal temperate lattitudes most annuals germinate or hatch as temp starts to rise in the spring, growing rapidly, reproduce, and then die before the end of summer - Perennials -- 1 generation over several years \- May have repeated breeding seasons at a predictable time (Eg. magpie), extended reproductive phases (Eg. primates & humans) which are tied less to the enviroment, or reproduce whenever the conditions are favourable [3) Timing of Reproductive Events:] Defined season vs resource availability - Fecundity (looks like "fertility") -- an organism's reproductive capacity (the number of offspring its capable of producing) - Parental investment -- the energetic investment into each offspring (Eg. egg size, seed size, amount of parental care) - Organisms can have many offspring each with a small energy investment, or few offspring each with a large energy investment \- Atlantic cod have millions of eggs (most of which starve/ get eaten) whilst humpback whale calves stay with for 10 months \- Orchids have a large number of cheap seeds, whilst coconuts & chestnuts have few but energetically rich seeds - A large brood size decreases the survival chance of the parents. - [Early Reproduction Strategy:] Eg. mice \- Short-lived, small in body size \- Reduces the risk of not reproducing at all & can maximise their reproductive events - [Late Reproduction Strategy:] Eg. elephants or large fish & sharks \- Long-lived, larger in body size \- Puts energy into growth to a larger size where mortality rates are lower \- Carries greater risk of not reproducing at all or to maximum capacity if death occurs early \- Increased offspring quality as older & more experienced parents can protect & provide for their young better - Trade-off between growth & reproduction, growth is usually greatly slowed in the reproductive phase - K Selection (K = Kareful) -- selection for traits that are advantageous in high-density populations \- Better competitors in more stable environments - R Selection (R = rapid) -- selection for traits that maximise reproductive success in uncrowded populations. Eg. desert locus \- Have the traits to rapidly respond to favourable environmental conditions or abundant resources - Not all populations go through boom/ bust cycles, but rather fluctuations can occur for biotic & abiotic reasons --------------------------- CONCEPT 14 -- POPULATIONS --------------------------- - Population -- group of individuals of the same species living in the same location, with the individuals: \- Relying on the same resources, influenced by similar environmental conditions & interacting with each other Properties of a Population: - [Boundary:] the spatial extend of that population \- Natural feature Eg. fish population in a lake, where the lake is the natural boundary or an island or even your gut \- Arbitrary (ones that we define) Eg. kangaroos in a national park as they can leave or enter as they wish - [Size (dynamic):] how many individuals are in that population and then also by how that number changes over time \- Things that effect this include births, deaths, emigrations, or immigration (individuals can come from somewhere else) - [Distribution:] the extend individuals are spaced within a population Eg. starfish are clumped whilst penguins are uniform - [Structure:] sex ratio & age structure \- Eg. typically more males than female kangaroos in younger age classes, whilst older kangaroos tend to be females - Population Ecology -- scientific study of populations in relation to the environment & resources \- How biotic (biological factors) & abiotic factors (non-biological factors) influence the abundance, distribution & composition of populations \- [Applications for Managing Populations:] this field is applied to understand: \- Threatened & endangered species management (how do we save species from extinction) \- Pest control, the dynamics of invasive species \- Harvested populations, working out the extend to which we can extract individuals from that population for human use \- Disease dynamics, both the spread of a disease through a population but also its impacts  Estimating Population Size: - [Full census --] count every individual, helps if species is easily identifiable or in a small area - [Sampling -- Estimate:] locate plots across a portion of the population range \- Count all individuals within plot \- Estimate average density, then extrapolate to the entire population - [Mark-recapture: ] \- Assumptions: marks/ traps are durable for length of study, marks don't decrease survival, probability of recapture remains consistent (not trap-happy or trap-shy) & it's a closed population (no deaths, births, immigration or emigration) \- Can use artificial marks (paint or tags) or natural marks (Eg. dorsal fin patterns on dolphins) \- Can us the abundance of different signs to estimate their relative abundance (Eg. burrows, or footprints)(much less intrusive) Life History Tables: summarize how survival & reproductive rates vary with age, sex and size of individuals in a population - Demography -- the study of the birth & death rates of populations and how they change over time - They follow the fate of a cohort (group of individuals of the same age) from birth to death, determine the proportion of the cohort that survives from 1 age group to the next, and the number of offspring produced in each age group - Survivorship Curves: \- [Type I:] high survival rates during early life, then high mortality after multiple reproductive cycles (high level of parental care) \- [Type II:] constant risk of mortality at all ages, common in reptiles & small mammals \- [Type III:] high morality early in life, with a high probability of survival after maturity, common in insects & plants \- Slope of the curve plotted on a log scale is an indicator of mortality, where steep slope = high mortality - Fecundity per surviving individual which is the number of young per year / number of individuals in that age class  -------------------------------------------- CONCEPT 15 -- POPULATION GROWTH & DYNAMICS -------------------------------------------- - Populations are controlled by the physical environment (Eg. pollution), biological interactions and dispersal & migration patterns like seen in whale migrations. - Exponential Growth: when populations aren't limited by resources, no real populations can sustain it for long periods of time - Logistic Growth: occurs when a population is limited by resources Population Dynamics: - Eg. Biological factor: A population may exceed its carrying capacity before leveling out, as some individuals have energy reserves so that when resources are limited, the population can still grow & reproduce. - Density-Independent Factors: change population size regardless of the density of individuals \- These are extreme events such as severe heat waves, storm events or pollution (Eg. oil spill) which may kill a large proportion - Density-Dependent Factors: change population growth depending on the number of individuals in the population \- Competition for resources as the population increases (intraspecific competition) Eg. invasive species maximise this \- Predation, predators may be attracted to areas with high densities of their prey \- Disease or pathogens may spread more easily in dense populations, causing a rise in death rate \- Some individuals survive better in a dense group, seen in predator avoidance - The dynamics of natural populations are often stochastic (random) as populations fluctuate from year to year & place to place - Environmental Stochasticity: unpredictable fluctuations in environmental conditions \- Eg. environmental variability in rainfall & temperature - Demographic Stochasticity: chance in birth & death of individuals caused by chance \- If the same birth rate & survival rate are modelled, the models change in population size might be slightly different each time \- The effects of it become important as population size decline Metapopulations -- group of geographically isolated populations linked together by dispersal - Populations have patchy distribution, and each species might be divided into groups of individuals (populations) - Eg. Metapopulation of Edith's checkerspot butterfly, where the species is divided into several populations, each confined to a patch of habitat that contains the food source of only 1 of 2 plant species - Source Population: support local population growth & can be net exporters of individuals (emigration) to other patches - Sink Populations: mortality exceeds births & populations are reliant on immigration to persist. - The theory of metapopulation dynamics can be used to conserve endangered species, as it allows individuals to disperse between source (donor) or sink (recipient) populations, thus spreading the risk of extinction across the entire landscape - Metapopulation persistence requires a balance between Colonisation & extinction of patches - Colonisation rate -- the proportion of unoccupied sites that become occupied per unit time - Extinction rate -- the proportion of occupied sites that go extinct per unit time TOPIC 4 -- COMMUNITIES & ECOSYSTEMS