BIOL1004 Main Lecture Notes (3) PDF

Unit 4: Mechanics of Evolution / Midterm Introduction (Day 1) Chapter 1 Scientific Methodology - the process of finding facts through tests and experiments 1.​ Observation 2.​ Question 3.​ Hypothesis 4.​ Prediction 5.​ Experiment 6.​ Analyse Results 7.​ Use Results to make new h...

Unit 4: Mechanics of Evolution / Midterm Introduction (Day 1) Chapter 1 Scientific Methodology - the process of finding facts through tests and experiments 1.​ Observation 2.​ Question 3.​ Hypothesis 4.​ Prediction 5.​ Experiment 6.​ Analyse Results 7.​ Use Results to make new hypothesis Chapter 56 The anthropocene and the great acceleration - due to the time in which humans have had a major impact on the environment, the human population and other parts of life have grown exponentially. This includes population, gdp, primary energy use, carbon dioxide, methane, nitrogen to coastal zone, surface temperature, forest loss, ocean acidification. -​ 37,000 species are in danger of extinction, with most being threatened like amphibians, conifers, reef corals. -​ ¼ of species on earth face extinction, by end of century this will reach 50% -​ 1 species is extinct every ~5 minutes The great 5 threats to our systems (HIPPO): H - Habitat destruction I - Invasive species P - Population P - Pollution O - Overharvesting Chapter 25: History Of Life On Earth (Day 2, 3 & 8) Hadean - Start of Time - 60:00 -​ 4.6 BYA the earth forms -​ Earth formed through dust hitting at fast acceleration -​ Earth was super hot, red, hell  -​ Meteor crashed into earth which then formed the moon -​ Due to the heat, the earth was fluid, heavier elements sunk to the core and had the lighter elements rose up above like hydrogen and helium making the early atmosphere -​ At the end of hadean, liquid water forms due to pressure -​ Possible RNA synthesis and folding ribosomes -​ * 3.7 BYA first evidence of life, 3.4 BYA had the first fossil, abiogenesis Archaean - 52:10 -​ First evidence of rock -​ Heat goes from 3x to 2x what it is now, plates slow down -​ Volcanoes start to form and magma flows -​ There is a weak magnetic field and earth is less stable -​ Earth is mostly water due to high condensation -​ Abiogenesis is the process that gives rise to life from non non, not fully understood -​ Process of increasing complexing in loving ​ Formation of earth ​ Reducing atmosphere, synthesis of small organic molecules ​ Molecular self replicating ​ Self assembly, protocell ​ This makes LUCA, all species including plants originate -​ *Oxygen forms called great oxygen event, around 2.7 BYA as a bi product of plants, making end of archean time -​ Oxygen is binded with iron and then makes iron oxide and allowed oxygen to go into the air due to a buildup of oxygen Proterozic - 32:37 -​ Higher oxygen level, changing atmosphere due to oxygen -​ Oxidizing atmosphere, reacts with UV rays to form ozone layer -​ Whole earth is covered in ice, 2.4-2.1 BYA influencing evolution -​ *~ 2 BYA came the rise of the eukaryotic cells -​ Eukaryotic cells rose due to a process involving: endosymbiosis ​ Starting with prokaryotes, without eukaryotes would not happen ​ Due to a build up of pressure, the nuclear membrane formed and endoplasmic reticulum ​ Bacteria was engulfed but not consumes, would evolve into mitochondria  ​ Break up of pannotia, creating new bodies of water like rivers allowing for new species ​ * 1.8 BYA - multicellular eukaryote fossil ​ * 890 MA - metazoans and sponge like porifera biomarkers ​ 575 MA - clear animal fossils ​ 555 MA - evidence of burrows (predators vs prey) Phanerozoic - 7:03 Paleozoic (541 - 252 Ma) Includes 6 time periods 1.​ Cambrian (541 - 485 Ma) ​ Rapid appearance of complex organisms ​ Bilateral symmetry and morphological complexity ​ Brains, sense organs forming, CNS, segmented bodies, limbs, better mobility ​ Armour, shells, exoskeletons, spines, protection and support from gravity ​ Big diversity, cambrian explosion, including most major animal phyla of today ​ Establishing the basic trophic structures and ecological dynamics seen today ​ Porifera, cnidaria, arthropoda, mollusca, annelida, brachiopoda, echinodermata, hemichordata, chordata all evolve ​ Colonization of land, issues arrived from gravity, oxygen, heat, water, reproduction, food 2.​ Ordovician (485 - 443 Ma) ​ Jawless fish ​ First primitive land plants 3.​ Silurian (443 - 419 Ma) ​ First jawed fish ​ First vascular plants ​ First terrestrial arthropods, insects and scorpions 4.​ Devonian (419 - 359 Ma) ​ Age of the fish ​ First forests, seed bearing plants ​ First tetrapods, flying insects 5.​ Carboniferous (359 - 299 Ma)  ​ Lush vegetation, coal swamps ​ Amphibians thrived, first reptiles 6.​ Permian (299 - 252 Ma) ​ Supercontinent pangea formed, causes issues like lost of shoreline habitat End of paleozoic: ​ Massive volcanoes ​ Enormous release of CO2, CH4, greenhouse gases ​ Ocean temperatures increased, reducing o2 solubility ​ Widespread ocean anoxia, massive dead zones ​ Excess co2 dissolved in seawater ​ Lowers pH (acidic) levels which harms organisms with calcium carbonate shells ​ Methane released due to warming in northern, due to permafrost, global warming ​ Damaging destabilizing ecosystems ​ Collapse of ecosystems, severely depopulated earth Mesozoic (252 - 66Ma) ​ Age of the reptiles ​ Pangea breaks up, more coastal habitat, forming of atlantic ocean ​ Dominant species include: scleractinian corals, dinosaurs, large marine reptiles, first flight, early lizards, birds and mammals ​ Ends with massive meteor that killed the dinosaurs, in mexico Cenozoic - Age of The Mammals (66Ma - Today) ​ Splits Into 3 different periods: 1.​ Paleogene (66Ma - 23Ma) ​ First time without dinos ​ rapid diversification mammals 2.​ Neogene (23Ma - 2.58Ma) ​ Emergence modern mammal families ​ Emergence of modern bird families ​ Spread of grasses ​ Early hominin ancestors 3.​ Quaternary (2.58Ma - Today)  ​ Age of the ice ages, alternating between glacial and interglacial periods, the last ending around 11.7K years ago, very thick ice around 2 km above the current location ​ Rise of humans (0.2 seconds ago), civilizations, agriculture Major Changes -​ This may occur through very small changes in genes Allometric growth ( rate) -​ Homologous structures -​ Change in rate of developmental events -​ Develop from zygote to adult, big morphological differences Heterochrony (timing) -​ When genes are turned on and off during growth -​ All about the timing of developmental events. -​ Ex. gills in a salamander being lost when turning into an adult -​ Paedomorphosis - when juvenile traits are kept to adulthood (ex. Humans from chimps) Gene sequence (spatial) -​ Hox genes!!!!!! -​ Different hox genes are responsible for head to toe body plan -​ Humans have 4 hox genes -​ Hox genes began with bilateral animals -​ Different species are made by simply turning off hox genes Evolution is NOT Goal Oriented Richard Dawkins, study of the giraffe neck: -​ In a video with Richard Dawkins, an evolutionary biologist and zoologist who had a giraffe's neck and studied the entire thing. -​ He found that giraffes have a weird nerve route, highlighting evolution quirks -​ The nerve loops and does not go in a straight line, going back to the ancestor fish -​ If there was a creator, they would have created a more straight nerve or a direct nerve, proving there is no creator -​ Evolution is based on past ancestors and builds on them, not a brand new structure -​ Evolution does not have a final goal, it's only going to the best route. Richard Dawkins, study of the eye -​ Before eyes, creatures had to bump into something in order to known what it was -​ Even darwin had a hard time thinking the eye came from nothing due to its complexity  -​ We know the eye evolved due to creatures now that have eye spots that have sensitivities to light vs darkness -​ Slowly the eye spot went from being flat to being curved over time, helping with what direction the light was coming from -​ Then the curved eye curved so much it got to a small hole, a pinhole camera sized eye which makes the image visible but still blurry -​ Then a blob of “gunge”/jelly is put in front of the eye and makes the image more clear, then when the jelly hardens it produces a better image -​ Then through natural selection over generation and generation that image becomes clearer to the vision we see today -​ Different species from the monkey to octopuses have nearly the exact same eye, even through evolution in different environments because the eye is the best solution no matter where. -​ The eye evolved in roughly 400,000 generations which is equal to around half a million years from a simple eye dot to the complex eye we have now Chapter 22: Descent With Modification (Day 3 & 4) Common Myths: 1.​ Evolution is a theory about the origin of life - False, evolution deals with how life changed after its origin 2.​ Evolution is like a climb up a ladder of process; organisms are always getting better - False, better (reproductive fitness) is linked to the environment not to progress 3.​ Evolution means life changes randomly - Partially, random mutations are the ultimate source of genetic variation, but current environment limit involuntary changes 4.​ Natural selection only involves organisms trying to adapt - False, this is lamarck's view, (pre-darwin): 1) inheritance of acquired characteristics (believed that changing charastics changes genes) 2) Use and disuse, body parts not used deteriorate over time and vice versa, believed this happens in a short time vs vestigial structures which go away over thousands of years 5.​ Natural selection gives organisms what they need - False, natural selection has no intention nor senses. Natural selection cannot sense what an organism needs. 6.​ Evolution is just a theory - True, but a theory is a very strong explanation of the natural world and supported by years and decades of individual evidence. Key Evolutionary Finds, Leading to Darwin:  1.​ Species have gone extinct - Cuvier 2.​ Time, lots of time has passed - Hutton and Lyell 3.​ Species change - lamarck 4.​ Trust your own observations - vesalius 5.​ Species have potential for unlimited growth but doesn't happen - Malthus 6.​ Individual vary within population - Darwin 7.​ Been practicing artificial selection (playing god) for 1000s of years - Darwin 8.​ Individuals with better suited traits to that habitable are more likely to leave more offspring than others - Darwin 9.​ If these better suited traits are hereditary - more likely these traits to become more dominant in further generations- Darwin 10.​ Source of variation is germ cell mutations - Modern scientist Example of Evolution: How Giraffes Got Their Long Necks: Lamark: ​ Giraffes with short necks, all no access to food, Giraffes think they can grow and stretch ​ Giraffes grow their necks through effort and grow their necks ​ It goes from short neck to long neck through a single generation Darwin: ​ There was a population of short neck giraffes, and within that pop natural variation occurs and some giraffes have slightly longer necks ​ Through environmental stress, constraint or behaviour it favours the generations with longer necks, producing more offspring ​ Then through generations, necks slightly start to grow in average until very long neck length ​ Now it gets to the point where necks that are too long become inconvenience, finding that goldilock spot Independent Lines of Evidence of Evolution: 1.​ Direct Observation ​ Two good examples, disease resistance and invasive species ​ Pesticide resistance, the problem today is not enough food supply, regional social institutions prevent proper distribution Pesticide resistance: -​ 1st generation: Toxic heavy metals, plant killing pests were dosed with heavy cyanide and 3% survived, which will leave to a population that can survive cyanide  -​ 2nd generation: DDT was sprayed on ecosystems, at the beginning 1kg did the job, but through evolution and adaptation by 1971, 64kg did the job -​ 3rd generation: compounds for the specific insect (ex. neonicotinoids), but can kill the wrong species like bees -​ 4th generation: RNA interference, GMOs, but causes issues with modification and food Pesticide Treadmill: -​ Using a chemical to kill pests, but some survive through adaptations -​ Those who survived have multiplied and therefore more chemicals are needed -​ More visible in pesticide and insects due to large population and short generations 2.​ Homology & Vestigial structures ​ The anatomy of the human hand who holds, seal who swims and bat who flies look the same ​ If we were created for our own function, you wouldn't copy from other animals that have completely different functions. ​ Same structure suggests there was a common ancestor who then evolved into different functionalities and species ​ Each species has the clavicle, humerus, ulna, radius, carpals, metacarpals and phalanges. There is a small difference of size but structure is the same, again proving common ancestor. Homologous structures: same structures but different function Analogous structures: same function but no common ancestor Vestigial structures: bones that are present but not used in a creature, evidence of common linkage in the past, ex: whales have legs which are useless but show they used to walk on land or snakes have tiny little legs used for sexual reproduction which use to be used for walking. 3.​ Fossil record ​ Transitional species: species in between 2 different species in between both that show characteristics of both. ​ Ex, pakicetus (50Ma): nostril moved from front in the beluga (0Ma) which is their blowhole, therefor there could be animals where the nostrils are in between which was found in Aetiocetus (25Ma) where the nostril was half way in the snout. ​ Fossils show amphibians evolved from fish, from swimming to walking on land through proof with the tiktaalik (375 Ma), Niel Shubin 4.​ Biogeography  ​ Distribution of species / ecosystems in geographic space and through time ​ Ex, Pangaea 220Ma forms, and breaks apart and shows that when north america and south america connect ( 3MA), This proves there were no horses in south america before the joining of the americas since horses evolved in north america ​ 50 MYA in north america the first horse ancestor ​ 35 MYA this ancestor looks more and more like the modern horse ​ 3 MYA the modern horse, equus and when america's connect, we also find the equus in south america Chapter 23: Evolution of Populations (Day 4, 5 & 6) Genetic Variation Makes Evolution Possible: ​ Evolution does not work on individual (lamarck's view) ​ Evolution works on populations (darwin's view) with variation, as exact copies can not vary Source of Variations: 1.​ Mutations within your germ line (sex cells), creating new alleles ​ Changes in heritable DNA, average load is 3.5ml aka 1B sperm ​ Every sperm has different variations, creating future variations, ¹⁄₅₀ to ⅕ of sperm carry mutations ​ Mutations can range from being neutral to positive to fatal 2.​ Chromosomal changes ​ During meiosis, variation in sperm/egg lines can occur like: a)​ Breakage of the chromosomes (translocation) b)​ Chromosome might be deleted (deletion) c)​ Duplication of parts of chromosome (duplication) d)​ A section can be inverted and spliced back in chromosome (inversion) e)​ Whole half of chromosome is deleted and remaining part is copied (isochromosome) f)​ Fusion of chromosomes from past ancestors, creating 1 long chromosome (fusion), shown in human chromosome #2, coming from #12 and #13 from the chimp 3. Sexual reproduction (13.4) Meiosis: ​ Prophase 1: -​ Recombination and crossing over  -​ Homologous chromosomes from each part align closely, form bivalent or tetrad -​ Inner chromatids are crossing over, creating diversity with same parents ​ Metaphase 1 and Anaphase 1: -​ Chromosomal tetrads line up on metaphase plate, very random in which direction they are pulled (Independent assortment) -​ Each homologous tetrad align in two ways -​ Tetrad separates, homologs pulled to opposite poles -​ Homologs pulled to opposite poles -​ 2n combinations, where n = haploid number of chromosomes, ex in humans n = 23, 223 = 200 billion trillion possible chromosome combinations. ​ Fertilization: -​ 246 unique chromosomal pairings, individuals can create variation for next generation How Much Variation Is There In A Population: 1.​ Find total population of each alleles, any convert into frequency (p+q)=1 2.​ Find genotypic frequencies (p+q)^2 = p2 +2(pq) + q2 ​ Heterozygosity (H) = 2(pq), measure of population variation/diversity at a single locus ​ With 16 individual, there are 8 purple alleles and 24 white alleles, therefore p=0.25, q= 0.75, genotype frequency: (p+q)^2 = 0.063:0.375:0.562, H=0.375 or 37.5% ​ For when more than 2 different alleles, add each where its 2xy. ​ Each individual can only have 2 alleles, no matter how many different alleles ​ Heterogeneity measured at a single locus does not represent heterogeneity for loci ​ To assess population heterozygosity, you need heterozygosity averaged over many loci, average heterozygosity (Have). Allelic diversity (A) is a measure of the average number of different alleles in a population Hardy-Weinberg Equilibrium No change(hardy-weinberg equilibrium): ​ For a given population that has no mutations, no immigrations, there is large population size and genotypes equal fitness, and completely random mating. There would be the same frequency of phenotypes through the same generation, p and q does not change  ​ This is called a neutral or null model of the hardy-weinberg equilibrium, in short evolution is not occurring With change: ​ If any of the following occur then it's not in hardy-weinberg equilibrium: ​ For a population, mutations do occur, immigration does occur, small population size, genotypes do differ in fitness and non-random mating (selective mating) then variations occurs and colours change ​ If values of allele frequencies (p and q) change from one generation to the next then at least one of the assumptions is not true and its no longer hardy weinberg equilibrium, in short changes allele frequencies make evolution at work, specifically microevolution. Mechanisms of Evolution (a)​Mutations - already previously covered (S6-12) (b)​Gene flow: -​ In a population of butterflies: -​ Originally its 50% and 50% with blue vs yellow in butterfly colours, then new population arrives -​ Now blue is 33.3% and yellow is 66.67%, a new storm occur and blue butterflies disappear -​ Now blue is 20% and yellow is 80% -​ P and q change because not in hardy weinberg equilibrium, which is called gene flow (c)​Genetic drift -​ Genetic drift says that through generation through random chances, some alleles are lost and eventually alleles become fixed -​ Small population allow for quick lose of genetic diversity -​ Bottleneck effect: starting with diversity and quickly lost of population, and end with only few alleles -​ Founders effect: when small groups leave, only their alleles are the ones present for future generations (d)​Natural selection -​ Through environmental stress like a predator, the animal that randomly is disguised with environment will survive -​ Alleles that don't get eaten and survive, repopulate giving rise to fish with better camouflage -​ Overtime, allelic frequencies will change due to environmental pressure.  -​ All about favouring better alleles to increase chance of survivability -​ Increases favorable traits in 3 different ways: i) Directional selection - Through time a pressure on a population causes evolution. (from one character to the next character(ex. Giraffe necks getting bigger or fish getting smaller) ii) Stabilizing selection - Population has pressure on both sides, stabilizing population in the middle (ex. Wilderbest hurds giving birth at the same time) iii) Disruptive selection - Pressure is in the middle, pushing the population to both ends (ex. Weather separating a bear into the grizzly and the polar bear) -​ Decrease unfavourable traits in 4 mechanisms: i) diploidy - Caring over the alleles but not expressing them ii) balancing selection - 2 or more phenotypes and environment keep them in the system: ​ Heterozygous advantage: (ex, sickle cell is recessive where blood cant carry oxygen and very sticky, blocking arteries. Die before able to reproduce). This can be helpful where needed like malaria is stopped due to some parts of sickle cell. ​ Habitat selection: Due to certain phenotypic expressions, predators will kill animals not matched to the environment (ex. Snails with stripes attracts bird that hunt snails) ​ Frequency dependent selection: phenotype that is most common is eaten way more than it should be, leading to that species population going down. This leads to the other phenotypes to grow and repeat. Predators will eat what is most common until it's unavailable. (e)​Non random mating → inbreeding -​ Can lead to loss of heterozygosity -​ Even with full self fertilization, heterozygous genes will half through every generation, eventually leading to full depletion. F(inbreeding coefficient) = 1 - (HO/He) -​ Definition of microevolution as changing frequencies of genes. Chapter 24: The Origin of Species (Macroevolution) (Day 6 & 7) Different Types of Species What is a species? -​ There are 25 different definitions but each don't cover all of the true terms of a species  -​ There is not one definition, its different for each type Morphological species: -​ Are distinct in form and structure from other groups -​ Used for fossil record, field guides -​ Similarities and differences can be misleading (ex, chinese vs indian muntjac) -​ Differences can be found through various ways like #chromosomes, song singing Ecological species: -​ Share distinct resources, same niche -​ Relevant towards ecosystem modeling -​ When species do the same thing, we can call them the same species *Biological species -​ Actually have or potentially of two species mating together and making a fetal offspring -​ If species cant mate then they are isolated species, different biological species -​ Can't be found through fossil record (morphological) Reproductive Isolation: -​ Accumulation of generic differences which prevents 2 populations from mating and creating fertile offspring -​ 2 different types of mechanism to prevent reproduction of species: 1)​ Prezygotic: -​ Prevents from mating due to the sperm and the egg from coming together i) Habitat/ecological - 2 pop. live in different in environments, don't cross each other ii) temporal - species in same location, but having different mating seasons iii) behavioral - species differ in communications, behaviours (different singing songs) iv) mechanical - Physical ability to reproduce, can't reach each other v) gamete - Different receptor proteins, sperm cant penetrate eggs 2)​ Postzygotic: -​ Sperm and egg do meet but the new species does not develop enough or sterile i) reduced hybrid viability - the developing fetus is aborted, chromosomes don't work ii) reduced hybrid fertility - Fetus is born but is not fetal and can't reproduce iii) hybrid breakdown -1st gen is fertile but 2nd is not Androdioecies species: -​ Mostly hermaphrodites, self fertilize -​ Mangrove killifish is an example Gynogenetic species -​ Only females in species, eggs are 2N diploid but fertilized by another species sperm to stimulate egg development -​ Amazon molly is an example that uses other fish species to stimulate eggs. Hybrid species -​ 2 species interbreed and produce fertile offspring for many generations Ring Species -​ Species that can be connected to another in a ring but the end species of the ring are reproductively isolated -​ Can breed with neighbours but not ends -​ Don't fit the definition of biological species Sub-species or breeds -​ Population groups within species -​ Share unique geo range and habitat -​ Distinguishable from other subdivisions -​ Dont not exhibit reproductive isolation -​ On the path to speciation Speciation -​ Bifurcation of an ancestral population into two species through evolution -​ Three different ways this occurs: 1)​ Allopatric speciation -​ Two populations through a process splits into 2 physically, can't maintain gene flow -​ Ex. Ancestral butterfly fish are separated by land, and by time both populations undergo natural selection, genetic drift and mutations. This creates the reef butterfly fish and the lined butterfly fish 2)​ Parapatric speciation -​ Population spread over discontinuity or strong gradient of environmental conditions -​ Ex. ancestral bear spread in NA and through climate the grizzly and polar were made -​ Each side undergo genetic drift, mutations and natural selection 3)​ Sympatric speciation -​ Same space, same time. Population is dispersed and within there is a pocket that become their own population -​ Ex. population only laid eggs on certain plants, creating difference in species  -​ Undergo the same 3 processes: mutations, genetic drift and natural selection Hybrid Zones -​ When species with incomplete reproductive barriers come into contact with each other -​ A trench was made, connecting 2 different oceans and 2 different species -​ Both species could theoretically mate if they mate together -​ Lowers fitness due to completion between different genotypes within organism Twin: 2 embryos that are independent being carried in the womb at one time Conjoined twins: twins whose bodies fuze and attach during development. Chimaera: 2 embryos merge at very early development, 2 sets of DNA, from each embryo. Hybrid: every cell of the body contains 2 different chromosomes, each from different species, causing display features of both species blended evenly together -​ Hybrids don't always lower fitness, sometimes it makes species grow faster, allowing for better adaptations to the environment Speciation Rates -​ Ranges from millions of years to one generation, from many genes to one gene -​ Ranges from species to species, depending on reproductive isolation Macroevolution: -​ large scale evoultion changes over a long time, above species level -​ Includes patterns of: a)​ Novel adaptations, leading to the new common ancestor b)​ Adaptive radiation, rapid diversification from a common ancestor c)​ Extinction of species groups, as per geological record Chapter 26 - Phylogeny and Tree of Life (Day 8 & 9) Carolus Linnaeus -​ Believed before any like darwin or lanark, that all species were of god and needed to organize them -​ Convinced could organize life into a single binomial naming system, to name everything -​ Used latin to name species, latin was used as a universal language -​ Created taxonomy - identifying and naming species, placing species into hierarchical classifications, reflecting morphological. Only looked at physical charastics  -​ Naming species baked on morphological similarities, is not hte same as common evolutionary ancestor, evolutionary theory was not known at the time -​ Had different nests/ different classes ( ) Humans as example: Kingdom - Animalia (move on own, eat on own) Phylum - Chordata (vertebrates/ tough tissue) Class - Mammalia (hair, milk glands) Order - primates (hands) Family - Hominids (smaller head, more complex interactions) Genus - Homo (mankind) species - Sapien New Better Updated Organization -​ We start with the common ancestor of all the species and then branch into different species -​ One issue in taxonomic is class reptilia are closely related to birds -​ When you have a group of species that dont include all of the species groups its called paraphyletic -​ Monophyletic - a common ancestor and all of its descendants (oppsitve of para) -​ Classes are now they are called clade, classifications are mainly about common ancestor -​ Phylogenetic tree - tree showing branching from common ancestor to current species, its a hypothesis given the best information, might change with further development -​ Systematics - researcher focused on classifying organisms with evolutionary relationship -​ Cladistics - building of a phylogenetic tree, using common ancestor i)cladogram: time- independent ii) phylogram: time -dependent Building a Phylogenetic Tree: ex. Gnathostomata Clade (Jawed vertebrates) Organization: 6 species: tiger, chameleon, gorilla, lizard, shark and human -​ Out group is agnatha, non jawed vertebrates, combined you get clade of vertebrates -​ Vertebrates traits: notochord, gill slits, dorsal nerve cord -​ Jawed vertebrates shared derived characteristics: jaws, bipedal(stand up), no tail, lungs, amniotic (internal water for fetus), hair -​ A 1 means present, 0 means not present  -​ Out group should not have any derived characteristics of ingroup, score of 0 Building the tree: -​ Start with common ancestor, with separation of outgroup (non-jawed) and in group( jawed) -​ Within ingroup, identify what separates the ingroup from the outgroup (jawed species) -​ Next get rid of species that has jawed, but no other charastics -​ Continue getting rid of species that has least amount of charastics -​ You will end up with a species that has all of the charastics, in this case its humans -​ This tree is called monophyletic tree: includes all descendents -​ Paraphyletic: ancestral species has some descendants but not all -​ Polyphyletic: not including common ancestor Making a Phylogram -​ Scenario: a species was left down to one owl, a female, people wanted to breed it with a male from another species that is very close, we need to identify which species is the most recent split for the best choice of a mate -​ Due to the time they used mitochondrial based phylogram to compare the differences between the species, the more differences the more different -​ In species 1, 8 differences, then 2, 8, 22, 22, 13 -​ They used the closest own species, and now there is a population 100 of the DNA of the original owl and the new species Principal of Maximum parsimony -​ Create a cladogram or phylogram -​ Can get very complex, creating different solutions Maximum parsimony: if there are multiple solutions, the one that is most likely to have happened is the simplest one to understand. Ex. ancestral species (AGTT), using a cladogram there are 3 species that came from the ancestor, with their own DNA. You then draw a cladogram, showing paths and divergence from ancestor to new species. -​ There are many ways to draw the cladogram, but the one with the fewest changes has the more likely chance of being true. -​ We count the changes in DNA for example from AGTT to AGAC has 2 changes -​ In image 1, there are 6 changes, in 2 there are 7, in 3 there are 7. This means that image 1 is most likely what happened