BIOM10002 Mastersheet 1 Page PDF

lOMoARcPSD|35623268 BIOM10002 Module 1, 2 & 3 Exploring Biomedicine (University of Melbourne) Studocu is not sponsored or endorsed by any college or university Downloa...

lOMoARcPSD|35623268 BIOM10002 Module 1, 2 & 3 Exploring Biomedicine (University of Melbourne) Studocu is not sponsored or endorsed by any college or university Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 MODULE 1: EXPLORING DIVERSITY Lecture 1: Reproduction DIFFERENT TYPES OF REPRODUCTION  All species reproduce and pass on their genetic material to the generation, they do this or else their species will die out Asexual reproduction Sexual reproduction  Requires one parents  Requires two parents  Offspring are genetically identical to  Produces genetic variation in offspring, parent (diseases are passed on and therefore offspring can better adapt to adapting to new conditions is hard) different environments or be more resistant to a disease  Time and energy efficient  Requires more time and energy (need to find a mate)  The population can increase rapidly  Population increases slower because when conditions are good more time/energy needed to find partner and only one sex can actually reproduce  Asexual reproduction is found in all  Sexual reproduction is only found in domains (bacteria, archaea, protista, protista, fungi, plantae and animalia fungi, plantae, animalia)  Organisms used to only undergo asexual reproduction but then they evolved and were able to undergo sexual reproduction ASEXUAL REPRODUCTION  Fission o Found in bacteria, archaea, protista, fungi, animalia o Occurs in unicellular and multicellular organisms o A parent cell divides itself into equal parts  Binary fission results in 2 cells  Multiple fission results in more than 2 cells  Budding o Found in bacteria, archaea, protista, fungi, animalia o Occurs in unicellular and multicellular organisms o A parent cell divides itself into 2 unequal parts o A small bud forms on the parent cell and breaks off to form a new organism  Fragmentation o Found in protista, plantae, animalia o Occurs in multicellular organisms o Fragments of an organism break off and then become a new organism Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Vegetative propagation o Found in plantae o Occurs in multicellular organisms o A new plant grows from a fragment of the parent plant  Spore formation o Found in protista, fungi, plantae o Occurs in unicellular and multicellular organisms o Parent forms many reproductive units called spores, these spores can grow into new individuals without fertilisation  Parthenogenesis o Found in animalia o Occurs in multicellular organisms o An unfertilised egg develops into an individual SEXUAL REPRODUCTION Alteration of generations  Alteration between haploid and diploid form is present in many multicellular protists and some fungi  Both haploid and diploid forms are multicellular  Diploid  spores & Haploid  gametes Sexual reproduction in fungi 1. Plasmogamy (mushroom) Cytoplasm between the cells have fused but the nucleus hasn’t fused 2. Karyogamy (in gills of mushroom) Nucleus fuse together and zygote forms 3. Meiosis Produces another haploid spore that can go an produce another organism Sexual reproduction in flowering plants (angiosperm)  There needs to be a transfer of pollen through abiotic or biotic factors o Abiotic: pollen can be transferred to another plant through wind or water o Biotic: plants have certain patterns on their pollen that only their pollinators can see, this attracts pollinators so pollination can occur Sexual reproduction in animals  External fertilisation: for aquatic animals only because gametes wouldn’t last very long in terrestrial environments  Organism releases their gametes at a specific time so that they will fuse in the external environment o They release the gametes in a periodic fashion, they release the gametes when there is minimal competition Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Internal fertilisation: for terrestrial and aquatic animals  Gametes fuse together inside the organism, typically the sperm fertilises the egg inside the female o Internal fertilisation can produce eggs or live young o Oviparous: animal that lays eggs  Embryo develops externally  Shell protects embryo and stops water loss  Nutrients for development are in the egg o Viviparous: animal that give produces live young  Embryo develops internally  Mothers body protects the embryo  Nutrients come from mother Lecture 2: Respiration DIFFERENT TYPES OF RESPIRATION  Aerobic respiration: organisms use oxygen to extract energy from food o Releases more ATP than anaerobic o This allowed for evolution of multicellularity and larger organism size  Anaerobic respiration: organisms don’t use oxygen, they use other compounds like nitrate or sulphur o Quickly releases energy o Can occur in low oxygen environments o Anerobic respiration was the first from of respiration to exist  Fermentation: anaerobic degradation of things like glucose into smaller molecules like lactic acid  Mitochondria evolved from endosymbiosis where a host cell (eukaryotic cell) engulfed an anaerobic prokaryote o Mitochondria evolved due to the benefits of aerobic respiration RESPIRATION IN MICROBES, FUNGI AND PLANTS  Bacteria and archaea: respire aerobically, anaerobically or both  Fungi: mostly aerobic but some are anaerobic, to get oxygen and release CO2 they use hyphae  Plants: obtain oxygen via diffusion through stomata (leaves and stems) or lenticels (stems of woody plants and some roots) RESPIRATION IN ANIMALS  Different animals have different systems to supply oxygen to cells and remove CO2  Different gas exchange types in animals o Direct diffusion  Small animals use this method Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Occurs across the outer membrane o Integumentary exchange  Exchange through skin  Gases diffuse directly across the skin into the circulatory system o Trachea  Trachea: network of tubes that branch throughout the whole body  Spiracles: openings to the trachea, can be open or closed when needed o Gills  Found in a cavity or externally  Gills are highly branched and folded thin tissues  Water passes over gills and oxygen rapidly diffuses across gills into the circulatory system o Lungs  There are 4 possible stages of respiration in animals o Breathing o Gas exchange o Circulation o Cellular respiration Lecture 3: Feeding AUTOTROPHS  We classify animals based on how they acquire their food  Autotrophs: synthesise the food they require for life  Autotrophs are the producers of organic energy for all other organisms o Present in bacteria, archaea, protista, plantae o Chemoautotrophs: bacteria that synthesise their own organic molecules using the oxidation of inorganic compounds (hydrogen gas, hydrogen sulphide) as a source of energy, rather than sunlight o Photoautotrophs: green plants, bacteria and algae that manufacture their required organic molecules from simple inorganic molecules, using sunlight as their energy source for photosynthesis o Anoxygenic photoautotrophs: use H2S as a source of electrons and have bacteriochorophylls instead of chloroplast o Oxygenic photoautotrophs: use oxygen from water in photosynthesis and produce oxygen as a biproduct  The earliest photoautotrophs were photosynthetic bacteria  Increased levels of oxygen favoured oxygenic photosynthesis  Eukaryotes engulfed photosynthetic bacteria, this resulted in the first plant cells (endosymbiotic theory)  Mitochondria and chloroplast came from the endosymbiosis theory  Mitochondria and chloroplasts have their own DNA but the genome size is reduced compares to prokaryotes Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Autotroph adaptations on land: o Roots to extract water and dissolved nutrients from soil o Vascular tissue for transporting water and nutrients o Water-resistant coating (cuticle) to minimise water loss to the atmosphere o Tissue for structural support o Diversity of leaf types and size for photosynthesis HETERTROPHS  Heterotrophs: unable to make their own food, they must consume other forms of life for nutrients  Heterotrophs are the primary, secondary and tertiary consumers o Present in all domains and kingdoms o Heterotrophs can be divided into multiple groups depending on what they eat  Heterotroph feeding strategies: o Diffusion – movement of nutrients through the cell membrane o Phagocytosis – engulfing food/prey, evolved specialised structures or cells to assist  These strategies cant support larger/more complex species o Filter feeding – feed by straining organic matter and food particles from water by passing it through a filter o Parasitism – parasites do not source food themselves, they feed from other species without killing them and without providing any benefit to the host o External digestion – feed by absorption of nutrients from the environment Lecture 4: Excretion DEFINING EXCRETION AND ELIMINATION  Excretion: the removal of waste products by an organism o Excretion regulates the internal environment in 3 ways  Controls cell/body water content  Maintenance of solute composition  Excretion of metabolic waste products and other unwanted substances  Secretion: the movement of material that has a specific task after leaving the cell/organism  Elimination: the removal of unabsorbed food that has never been part of the body (poo)  Respiration: the process by which an organism exchanges gases between themselves and the environment Excretion and elimination  Are important because an inability to remove waste can lead to disruption of cell membrane, inefficient metabolism and this may lead to death  Excretion and elimination can be passive o Passive transport is where solutes cross the membrane without the involvement of a specific transport protein Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 o Movement of solutes occurs due to the chemical gradient of the solutes (osmosis or diffusion) o Common in bacteria and some aquatic plants  Excretion and elimination is mostly active o Species have specialised cells/organs that have evolved to assist with excretion and elimination o Active transport of waste allows organisms to be larger and more complex Specialised cells that assist with excretion in plants  Guard cells o Located on the outer surface of leaves and stems o Produced in pairs with a gap between them called the stomatal pore o Involved in gas exchanged and assist with controlling water loss o Stomatal pores open when the plant has lots of water and the guard cells are swollen o The stomatal pores close when water availability is low and the guard cells shrink Specialised cells that assist with excretion in animals  Flame cells o Specialised excretory cells found in freshwater invertebrates o Flame cells function like mammalian kidney – they remove waste material o Bundles of flame cells = protonephridia Coelom  Specialised organs need space  Coelom are fluid filled so they can be used as internal support  The separate internal processes from gut  Allows transport of fluids (circulatory and excretory systems)  Provides space for development of internal organs  Enables increased body size EXCRETION AND ELIMINATION IN BACTERIA, FUNGI AND PLANTS Excretion in protists and early eukaryotes  Single celled organisms have just one cell and they have no specialised organs  The majority of waste and biproducts of metabolism are eliminated by passive diffusion and osmosis Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Active transport of waste occurs through specialised membrane channels or they are expelled directly Excretion in fungi  Fungi have no specialised organs to excrete waste  Some waste and biproducts of metabolism are eliminated by passive diffusion and osmosis  Active transport of waste occurs through specialised membrane channels or they are expelled directly using a similar method to exocytosis with food vacuoles Excretion in plants  Transpiration: gaseous waste and water are excreted through stomata, lenticels of the stem and the outer surface of the stem  Storing: some organic waste is stored in plant parts such as barks and leaves. Cells storing the waste in barks and leaves will eventually die and fall off  Diffusion: aquatic plants excrete metabolic wastes through diffusion, terrestrial plants excrete wastes into the soil o Water and soil nutrients diffuse into plants through their root hair cells o Water moves from an area of high conc to low conc because root hairs are partially permeable (this diffusion is called osmosis) o Root hairs increase SA for water and nutrient uptake and excretion facilitating process EXCRETION AND ELIMINATION IN ANIMALS Nitrogenous waste  Protein is required by heterotrophic animals and metabolism of proteins produces nitrogen waste  The form of nitrogen waste that each animal produces will vary and organs that animals have evolved to process nitrogen also vary  Nitrogen waste is a problem o To solve this problem animals convert excess N into ammonia, urea, uric acid and guanine o Most aquatic species excrete ammonia o Most terrestrial species excrete urea or uric acid o Spiders excrete guanine Advantages and disadvantages of different N products (ammonia, urea, uric acid and guanine)  Ammonia: o There is one nitrogen molecule present in one ammonia molecule o Ammonia requires lots of water for excretion o Ammonia is very toxic however, it is also very soluble and very little energy is required to synthesise it  Urea: o There are 2 nitrogen molecules present in one urea molecule o Urea is less toxic and requires less water for excretion o The synthesis of urea is more complex, and it requires 4 ATP  Uric acid Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 o There are 4 nitrogen molecules present in one uric acid molecule o Uric acid is highly insoluble and non toxic so it doesn’t require a lot of water to excrete o But the synthesis of uric acid is very complex and requires 24 ATP  Guanine o There are 5 nitrogen molecules present in one guanine molecule o Guanine is almost insoluble and it can be excreted with very little water loss o But there is a high energy cost needed to excrete it which is why only one group uses guanine Excretory organs in animals body  Excretory organs transport waste from the coelom to the exterior  In birds and reptiles excretion and elimination occur from the hindgut via a single opening however, mammals have a separate opening for excretion and elimination  Hindgut o In insects, bird and reptiles the hindgut is involved in both excretion and elimination o Nitrogen first moves into the hindgut before excretion and is mixed with faeces  Kidney o The primary excretory organ of vertebrates o Other organs like the skin, gills and gut assist with solute and water regulation  Liver o Breaks down many substances in the blood including toxins o Also assists with the breakdown of red blood cells Lecture 5: Movement DEFINING MOVEMENT & THE ARLIEST ADAPTATIONS The process of moving  Individuals move to find food, mates, suitable habitats or to escape predators  Movement is essential for survival  Evolution has shaped the types of movement and mechanisms that organisms use Passive movement  Advantages: o Involves little or no energy because you are relying on the environment to move you around o Organisms can move passively through water and air very easily o Some species attach themselves to hosts  Disadvantages: o You have little or no control over where you end up o May end up in an environment that is not good for your own development  Some species use both active and passive movement Active movement Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Advantages: o More control of where they move o Organisms actively move through all environments  Disadvantages: o Energy is required for movement o The energy an individual uses for movement could be used on other things like cellular maintenance or reproduction Moving in water  Living in water has many advantages o Support o Hydration o Nutrient rich o Environmentally buffered – water doesn’t change its temperature as much as terrestrial environments  Movement in water is challenging o Strong currents – you can end up in an environment that you are incompatible with o Buoyancy – maintaining position requires energy or specialised structures o Water levels – might fluctuate  Structures that species have evolved to move in water o Cilia and flagella o Feet like structures o Fins and flippers in birds and animals Moving on land  Living on land has many challenges o Oxygen in air – need to evolve ways to capture air o Lack of water – dehydration is a major problem o UV radiation – risk of DNA and cell damage o No support – species require structures to support themselves on land o Energy hungry – there is no passive movement on land, you must use active transport o Terrestrial ecosystems are complex and vary dramatically  Structures that species have evolved to facilitate active movement on land o Cell walls o Vascular tissues o Lignin and bark o Seeds or spores o Legs Moving in air  Air is the safest environment due to the lack of other species which move via air however, it is also very challenging to move in o Gravity – adaptations required to ensure an organism is lifted and does not plummet down Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 o Strong wind currents – can push you into a suboptimal environment o Extremely energy hungry – flying requires the use of huge muscles, this energy could be used for other things like reproduction  Adaptations required to move in the air o Light weight – however, you may get blown away by the wind o Produce lots of seeds – chance of landing in a good environment is low so if you produce many seeds there is a chance that seed can move to better environment o Large SA needed for lift – helicopter seeds, wings, gliding membranes o Enlarged muscles needed for flight Early adaptations that facilitate active movement  3 main adaptations in prokaryotes and eukaryote protists: o Cilia – tiny hairs that cover the outside of the cell  Often found on unicellular species  Unicellular species that use cilia tend to be larger than species that use flagellum  Move faster than species that use flagellum  Cilia beat in a co-ordinated movement across the cell o Pseudopods – false feet that move out in specific directions  Unicellular amoebae alter their cell shape by pushing cytoplasm outward to produce false feet  Organisms can have multiple false feet projecting from the cell in different directions, they use these to move in particular directions  When food is in scare supply, individual amoebae can combine to form a single travelling colony o Flagella – longer hair like structures that are propelled around  Its primary function is locomotion (moving from one place to another)  Can also function as a sensory organelle MOVEMENT IN WATER AND THE TRANSITION TO LAND Active propulsion Cnidarians  Adult jellyfish move through the water by expanding and contracting their bell-shaped bodies to push water behind them  Muscles assist in this process  This is a very energy efficient way to move through the water Molluscs (squid, octopus, cuttlefish)  They take in water through their mouths and then contract their body to push the water through their funnel thus achieving forward propulsion  Muscles assist in this process  Tentacles also aid in movement: they control the direction of movement Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 Movement in water and on land  Molluscs can move on water and land  Molluscs have: o Mantle – body on their back, in some species this forms a shell (eg. Snails) o Muscular foot – used for moving, feeding and manipulation Adapted for movement on water and land  Annelids can move on water and land  Marine worms (free swimming and sedentary) and earthworms (live in soil, react to vibrations) Evolved in the water and moved onto land  Chordates have: o Notochord o Dorsal nerve chord o Myomeres (segmented muscles) Cartilaginous V Bony fish  Cartilaginous fish have: o Large liver filled with low density oil (need to swim to maintain buoyancy) o Cartlidge which is lighter than bone o Pectoral fins which provide dynamic lift  Bony fish: o Have swim bladder for buoyancy o Swim bladders are evolutionary closely related to lungs o The evolution of sturdier fins:  Most bone fishes have fins made of long rays of bone  Some fish developed more substantial bones in the fins which can support the weight of the fish MOVEMENT ON LAND AND HOW ANIMALS TOOK THE AIR Evolution of insect flight  Wings most likely evolved from gills Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Wings from early species aided in locomotion across water surface The evolution of mammals and a change of stance  Dinosaurs come from the same lineage as crocodiles, but dinosaurs walk upright unlike crocodiles  Mammals evolved from reptiles and mammals also walk upright  Hip joints and upper limb bones changed in mammals and dinosaurs, this caused a change in stance How do humans walk upright?  Humans underwent some changes to their skeletal structure o Big toe reduced o Pelvis shortened o Femur bends inwards, knee straightened, patella central to joint o Connection with spinal column on the skull o Less robust upper arm Lecture 6: Fossils THE FOSSIL RECORD AND EVOLUTIONARY TRANSITIONS  Fossils are the preserved remains or any preserved traces of a once living organism  Organisms are more likely fossilise if: o They have bones or hard structure o The organism is quickly covered after it dies o The remains are in an environment with no oxygen o The chemistry of the environment doesn’t dissolve the organism How do we date fossils?  Relative dating o Stratigraphy: use the layers of rock to determine which layer is the oldest, layers that are found further down are older o Index fossils: index fossils have a known date so if a rock is found together with an index fossil you can assume the rock is from the same time as the index fossil  Absolute dating o Radiometric dating methods: based on the decay of certain elements o Carbon 14 decays to Nitrogen 14 o So the older a fossil is the more nitrogen it will have Major evolutionary transitions  New units of reproduction  Division of labour/cooperation  Development of more complex units Historic mass extinctions  The rate of origination and rate of extinction can be used to understand diversity and identify adaptive radiations and mass extinctions Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  The fossil record helps to determine the rate of origination and extinction Adaptive radiation  Adaptive radiation is when evolutionary lineages undergo exceptionally rapid diversification into a variety of lifestyles or ecological niches o There is one common ancestor that has rapidly diversified into a lot of different forms and species Mass extinction  Mass extinction is when the rate of extinction increases significantly resulting in substantial loss of diversity or when rate of origination drops  Extinctions can occur from many causes eg. Change in climate, habitat loss or predation Human causes of extinction  Many human actions can lead to extinction o Habitat loss eg. deforestation o Species introductions eg. Introduction of a predator that may affect native species o Pollution o Overexploitation eg. Hunting too much o Climate change  Extinction of one or two species can have a cascading effect and this could lead to the collapse of an ecosystem MODULE 2: WHAT IS EVOLUTION Lecture 7: Introducing evolution INTRODUCING MICROEVOLUTION  Natural selection: a mechanism that can lead to evolution. Phenotypic differences among a population causes some of them to survive and reproduce more effectively than others o Individuals with phenotypes most suited to the environment will be more likely to produce offspring o This drives evolution o Some factors that may contribute to natural selection are:  Competition (mates, food and resources)  Selection (disease, predation)  Environment (climate, ecology)  Evolution: the cumulative change in a population or species over time  Macroevolution: studies major evolutionary changes among large taxonomic groups over long periods of time o Macroevolution refers to all the changes between ancestors Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Microevolution: studies the evolutionary ‘agents of change’ that shape the genome within a population o Examples of agents of change:  Natural selection – survival & reproduction of the fittest  Mutation – the ultimate source of variation  Sexual reproduction – recombination of genes, mate choice  Genetic drift – changes to allele frequencies based on chance  Gene flow – migration, movement and hybridisation THE HARDY-WEINBERG THEOREM  HW theorem gives us the genotype frequencies expected for any possible set of allele frequencies  Allele frequencies will not change from one generation to the next o They remain in equilibrium and dominant alleles can’t over run recessives  Allele frequencies always sum to 1 o B allele = p o b allele = q o p+q=1 Calculating genotype frequencies when allele frequencies are known  Frequency of allele B = 0.7 = p  Frequency of allele b = 0.3 = q  Mice are diploid and require 2 alleles  Genotype frequencies o Probability of being BB = p2 = 0.7 x 0.7 = 0.49 = 49% o Probability of being bb = q2 = 0.3 x 0.3 = 0.09 = 9% o Probability of being Bb = 0.7 x 0.3 = 0.21 o Probability of being bB = 0.3 x 0.7 = 0.21  Probability of being heterozygote = 0.21 + 0.21 = 0.42 = 42% Expected genotype frequencies  Hardy-Weinberg theorem p2 + 2pq + q2 = 1 (0.49 x 0.49) + (2 x 0.7 x 0.3) + (0.3 x 0.3) = 1 o Expected frequency of BB = p2 o Expected frequency of bb = q2 o Expected frequency of Bb = 2pq Calculating allele frequencies when genotype frequencies are known  Assume a population size of 1000  Frequency of genotype BB = 0.49 = 0.49 x 1000 = 490  Frequency of genotype Bb = 0.42 = 0.42 x 1000 = 420 Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Frequency of genotype bb = 0.09 = 0.09 x 1000 = 90 Finding p and q  Allele frequencies o Frequency of allele B  p = freq. (BB) + freq. (Bb) BB - Bb(not plus)  because only half the population of Bb have the B allele  p = 0.49 + (0.42) = 0.7 o Frequency of allele b  q = freq. (bb) + freq. (Bb)  q = 0.09 + (0.42) = 0.3 HARDY-WEINBERG THEOREM (OPBSERVED AND EXPECTED PHENOTYPES) Allele frequencies remain in equilibrium if the 5 unrealistic conditions are met 1. No migration o We can’t have different alleles entering the population to disrupt the existing alleles 2. No mutation o We can’t have mutations that change white mice into brown mice o Can’t have mutations creating new phenotypes either 3. Equal fitness (no selection) o If the brown and white mice lived together in an environment where there was brown soil o Brown mice will have an advantage and predators will eat more of the white mice 4. Infinite population size o Allele frequencies in small populations can change quickly by chance events o So, for allele frequencies to remain in equilibrium we need an infinite population 5. Mating is random o If white mice only mated with other white mice there will be a higher frequency of white mice in the population  According to the Hardy-Weinberg theorem if we adhere to the 5 steps then over generations the frequency of alleles remains exactly the same Do observed frequencies match expected frequencies?  Calculate allele frequencies using population genotypes Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Use Hardy Weinberg equation to calculate the expected genotype frequencies  Apply a simple chi-squared test  Check to see if X2 value is significant o Degree of freedom (d.f.) = number of alleles – 1 Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  P AA > SS  We can use relative fitness to find the selective advantage of being a heterozygote Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 Lecture 10: Agent of change – Genetic drift GENETIC DRIFT  Genetic drift involves random changes in allele frequencies and it can sometimes cause an allele fixation in small populations o Alleles become more or less random simply by chance (no allele is favoured) o During genetic drift allele frequencies change due to sampling errors. Small populations will be more biased Genetic drif in small populations  Genetic drift occurs in all populations, but the effects of genetic drift are more noticeable in small populations  Allele fixation occurs quickly  There is a larger probability of an allele changing frequency Genetic drif in large populations  Effects of genetic drift are not that noticeable  Populations don’t need to be infinite, but they just need to be large enough so that random sampling effects do not impact the allele frequencies  Larger populations will reach the fixation of an allele slower  There is a smaller probability of an allele changing frequency Experimental evolution by Buri  Allele frequencies change with each successive generation  One allele can reach a frequency of 1  We can’t predict which allele is fixed BOTTLENECKS AND FOUNDER EFFECTS Genetic bottleneck  Caused by events that reduces the size and genetic diversity of a population significantly  These types of events are random, and they are not related to natural selection (eg. Bushfires)  Populations impacted by genetic bottle neck are smaller and they contain a random sample of alleles that were present in the original population Why is genetic bottleneck an issue?  Increased homozygosity Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Fixation of alleles occurs quickly  Less genetic diversity Founder effect  Caused by a small number of individuals founding a new population  Random differences in allele frequencies occur when a small colony splits from a large population o Genetic drift can act on the small colony causing a completely different population to form  The chance of losing alleles after a bottleneck or founder event depends on their initial frequency and the population size o In large populations the chance of losing an allele randomly is small  After a bottleneck or founder event the population will recover its size quickly, but genetic diversity will not recover GENE FLOW  Gene flow: the transfer of genetic information from one population to another through migration, movement and hybridisation o Hybridisation: interbreeding of individuals from different populations or closely related species  This can alter allele frequencies, introduce new genetic variation or reintroduce existing genetic variation  Barriers between populations can influence the connectivity between populations and the extent of gene flow between populations o Migration + less porous barrier = less connected o Movement + more porous barrier = more connected Impact of gene flow on the gene pool  The impact of gene flow depends on: o The level of migration, movement or hybridisation (m) o The genetic difference between populations Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 m = number of migrants/total number of animals After one generation of migration the resident population will have p + Lecture 11: Agent of change – Migration SPECIATION  Speciation: the evolutionary process by which new species arise through reproductive isolation  It causes one evolutionary lineage to split into 2 or more lineages, and sometimes these 2 new species will be unable to mate due to reproductive barriers  Reproductive barriers prevent gene flow and enable speciation Allopatric speciation  Speciation that occurs in different geographical locations  Pre-mating isolation: eg. Geographical and behavioural isolation o Isolating barriers that stop gene flow before sperm or pollen can be transferred to other species o Geographical isolation (allopatric speciation)  When something like a river separates a population into 2 groups  These two groups will experience different agents of change and will hence develop different DNA, phenotypes and behaviours  When the geographical isolation is removed, individuals from the two groups will be unable to mate with each other  reproductive isolation Sympatric speciation  Speciation in the same location  Pre-zygotic isolation: eg. Mating time and ecological differences o Isolating barriers that stop gene flow before fertilisation of the zygote (prevent two species from mating)  Post-zygotic isolation: eg. When 2 species mate and the fertilised egg fails to develop or when a hybrid offspring is sterile o Isolating barriers that act after a zygote begins to develop Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 SPECIES  Biological species concept: species are groups of interbreeding populations that are isolated from other groups  Phylogenetic species concept: species are the smallest possible groups whose members are descended from a common ancestor and who all possess defining characteristics that distinguish them from other groups  Ecological species concept: a concept that species are sets of organisms that are adapted to a particular set of resources/ecological niches Why is it useful to define a species?  Conservation (categorising endangered species)  Food (classifying fruits and vegetables  Safety (classifying between venomous species)  Medical (so we know how to diagnose and treat infections created by certain species)  Recreational (catch limits when fishing) ADAPTIVE INTROGRESSION  Hybridisation: when individuals from two different species mate  Adaptive introgression: inheritance of beneficial variation from related species that accelerate adaptation survival in new environments o During hybridisation adaptive introgression occurs. One species will inherit alleles from the other species that are beneficial and help with survival Lecture 12: Molecular genetics and Genomics Genes  Genes that code for protein are involved in complex biological, cellular and molecular functions that together contribute to a phenotype  Multiple genes can contribute to a phenotype  All genes are required but some genes may be more important than others  The alleles that influence or improve a phenotype may be subject to selection Molecular genetics + Genomics  Molecular genetics and genomics involve the sequencing and analysis of an organism’s genes and entire genome  Molecular genetics: when you study DNA sequences that encode specific genes in order to understand function of the genes better  Genomics: the study of the DNA sequences of an organism’s genome o Genome sequencing  Extract the DNA  Create DNA library  Sequence  Assemble data o Genomic analysis of many individuals  Collect samples, create libraries, and then sequence Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Investigate one gene or the entire genome  Identify SNP’s and other genetic variation MODULE 3: ENERGY, MATTER, AND INFORMATION Lecture 13: What is life – Organisms in the context of energy, material, and info flow EXCHANGE OF ENERGY, MATTER, AND INFORMATION Schrodinger  Food we consume  negative entropy o The food has a high level of order and it is used to maintain order within the organism o Food compensates for the disorder that is inevitably forming in the organism due to the random smashing of molecules o This random smashing of molecules may cause an organism to fall apart if left unchecked  Aperiodic crystal (DNA) o A molecule that can remain ordered despite all the disorder o Can hold all this information and pass it onto future generations Entropy and Maxwell’s Demon  Entropy and information are closely related concepts (they are opposites)  Goes against the second law of thermodynamics  Demon only allows fast molecules to pass through the barrier o This creates a temperature gradient which can be used to do work o No energy is expended to create this gradient Swimming against the entropy  Temperature is measure of heat and heat is a form of energy  Heat represents the energy of molecules flying around in space  If you heat up a patch of molecules the molecules will start to move faster o Faster moving molecules will bump into slower ones and pass on their energy  Entropy is the tendency molecules have to spread energy out  Energy that is spread out this way is lost and not good for doing work  Second law of thermodynamics: molecules have a natural tendency to spread out their energy evenly over time Living organisms  According to the second law of thermodynamics complex organisms should fall apart o However, if there is work going on then complex organisms will not fall apart Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 o Work is a type of energy like heat but unlike heat, work is the energy of molecules that are all moving in the same direction (in heat molecules move randomly) o This ordered movement helps complex organisms to maintain order and not fall apart  The energy organisms release from metabolism is used to do work on the molecules o Organisms steal order from their environment (eg. From food) to increase their own level of order and complexity  This is not a breach of the second law of thermodynamics because: o Not all the energy from food is going into doing the work o Some of the molecules receiving the energy shoot off in random directions and this heats up the body of the organism  This heat will spread from animal into environment. This decreases order of the environment  Metabolic rate: the rate of heat production of these random molecules  Organisms have a purpose to always remain the same and stay in order o To do this, organisms must find food, water, make sure it doesn’t get too hot or cold o The greater aim is to pass on information to future generations Lecture 14: Building bodies – Metabolism & the theory of growth METABOLISM OF ORGANISMS  Thermodynamics: the study of the exchange of heat and how thermal energy is converted into other forms of energy  Flow of energy going in = flow of energy going out + energy stored in the animal Measuring metabolic rate  We can measure the metabolic rate as heat production or oxygen consumption  It reflects a whole series of processes that relate to how the organism becomes larger and more organised  Basal metabolic rate: used to compare the metabolic rate of endothermic animals that release heat  Requirements: o Animal is not moving o Not digesting o In its thermoneutral zone (animal doesn’t have to produce heat to stay warm) o Is inactive o Is an adult (this makes sure no heat energy is wasted on growth of the animal) o Is not reproducing  Standard metabolic rate: used to compare the metabolic rate of ectothermic animals who do not generate extra heat (their body temp fluctuates with the environment) Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Same requirements as MMR except instead of thermoneutral zone the body temp of the organism must be known  Resting metabolic rate: can be used for endotherms or ectotherms  Field metabolic rate: the metabolic rate for an organism behaving naturally in the wild Temperature and metabolic rate  Homeothermic endotherms: organisms that can generate body temp above temp of environment o Changing environment temp has no effect on body temp  Heterothermic ectotherms: organisms that match their body temp with the temp of the environment o Increasing environment temp increases body temp Body size and metabolic rate b=¾ Metabolic web  How are metabolic processes connected? o Food comes into the organism through the process of feeding Assimilation + Digestion, They o Assimilation (digestion) converts the food into reserves this is not 100% efficient and are not the same thing some waste product comes out of the organism o The reserve is used by the body to fuel growth, maturation and reproduction Lecture 15: When bodies fall apart – Environmental limits  Organisms need to find a suitable environment to reproduce and produce enough offspring to replace the individuals in the population that are dying  Metabolic niche: the requirements in an environment that an organism needs to reproduce What happens when animals get too hot or cold Temperature and ectotherms  Organism always has fluctuating body temp  Temp being too hot or too col can impact cell membranes and enzymes in the body o Temp becoming too high  enzymes may denature o Temp can also indirectly impact enzyme function by impacting the fluidity of cell membranes that have enzymes embedded into it Behavioural thermoregulation  Behavioural techniques are used to help ectotherms to lose/gain heat Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268 o Eg. Animals moving into different environments to maintain an optimal temperature o Moving into/out of shade, pointing their body towards sun rays to increase temp Temperature and endothermy  Organism has the ability to generate heat for thermoregulation  Endotherms also utilise behavioural techniques to lose heat  All endotherms and ectotherms have a thermal response curve  differs between species  Torpor: when an animal reduces it body temperature and metabolic rate to survive long periods of reduced food availability Lecture 16: Receiving information INFORMATION ABOUT CHANGING ENVIRONMENT  Signals and cues provide organisms with information about their constantly changing environment Changing environments  Organisms require information about their local environments o Sensory modality is different for each species, and it depends where it lives and its lifestyle o An organisms environment changes constantly and organisms need to acquire information about those changes so it can behave accordingly Spatial and temporal variation  Food is distributed throughout space and needs to be detected by animals  Animals must also be aware of potential predators to evade the premises if necessary  Selection must favour the sensory mechanisms that allow signals and cues to be detected  Chemicals (signals and odours) transmit information SENSORY MODALITIES  Information is conveyed through diverse sensory modalities or channels  Chemical modality (olfactory): there must be a physical interaction between odour and receptor 1. Production and dispersal of pheromones 2. Pheromones intercepted by antennae 3. Pheromones activate receptors  Electrical modality: works well in aquatic environments because electricity is more easily transported through water than air o Sharks can detect the location of a fish even when they are constrained in sand  Visual modality (light): the ability to see varies across species and many depend upon eye size, the bigger the eye the better the vision Downloaded by Bucket Beaver ([email protected]) lOMoARcPSD|35623268  Magnetoreception: bacteria and many animals detect and respond to the magnetic field, allowing them to orient over long and short distances o Allows birds to know when to migrate  Mechanical: web building spiders use vibrations, transmitted along the flexible silk, to detect the location and size of prey that are arrested by the web  Sound frequency: echolocation  objects in space are located by directing sounds at them and then picking up on the echoes o The longer the time interval until the echo the further away the object SIGNALS, CUES AND HOW TO RESPOND  Signal: any act or structure that influences the behaviour of other organisms, signals evolve specifically for this purpose  Cue: an incidental source of information that may influence the behaviour of a receiver, cues do not evolve for this specific purpose though  Signals are only effective if they are detected  Signals and the information they provide, may not reach their intended receiver  Signals are strategic and effective  Each signal has an intended purpose  Cues may be a by-product such as faeces Lecture 17: Deceiving information EAVESDROPPING  Signalling is physiologically costly, and it can also reveal the location of the signaller and hence providing a cue for a natural enemy o Physiological  When producing signals there is a drain on resources during growth or during immediate production of signal o Exploitation  Signals or cues may be intercepted by predators or parasites (unintended receiver)  Unintended receiver uses the signal of others for its own benefit CAMOUFLAGE AND MIMICRY  Organisms exploit information in the environment, through camouflage and mimicry, to avoid or enhance detection  Camouflage reduces the likelihood that an organism will be detected or recognised o Masquerade: a type of camouflage that prevents an animal from being recognised by making the animal look like an uninteresting or unimportant object (leaf or stick)  Benign mimics: when an animal resembles a dangerous or toxic model o Predators avoid eating the poisonous model and mimic COEVOLUTION AND ARMS RACES Downloaded by Bucket Beaver ([email protected])  The evolution of communication may involve antagonistic coevolutionary processes, depending upon the relationship between signaller and receiver  Coevolution is a process involving a pair of species where changes in the traits of individuals in one species causes reciprocal changes in the other species over evolutionary time Lecture 18: Transferring information REPRODUCTION AND INFORMATION  An organism requires information to develop from egg to adult  Reproduction allows that information to be converted from one individual to another Sex as a source of conflict  Conflicts over choice of partner and number of partners  Sexual selection: competition between members of one sex for reproductive opportunities with the other sex o Mate choice and male-male competition are part of sexual selection and they both involve signalling  Males and females run in to conflict of interest o Females would benefit from polyandry (being able to mate with more than 1 male throughout their reproductive cycle) o Males, however, favour sexual selections that prevent polyandry Reproduction requires care  Parental care, the provision of nutrients or safety from the elements and natural elements, ensures th B OM M MOD OM D HOW m m m m