Evolution & Molecular Systematics PDF

1. O Introduction Evolution-process by which populations adapt to environment overtime by Natural Selection. Taxonomy-Morphologic relationship between...

1. O Introduction Evolution-process by which populations adapt to environment overtime by Natural Selection. Taxonomy-Morphologic relationship between organisms. Systematics - Taxonomy related to evolutionary processes. Molecular Systematics- Use of molecular data to reveal evolution processes. Classification - Naming Species to reflect the above. · Centre of Evolution is adaptation. · Alleles ; form of the same gene.  1. 1 Brief History of Evolutionary Biology Aristotle & essentialism 350BC · Aristone & · Species never Change. essentialism 350BC First Classified blooded vertebrates & bloodless Invertebrates. · · Essentialism does not know about genetic variation. Carlvon Linnes · Carl von Linne 1753 · Jean Baptiste Baptiste Lamarch & transformism Sean 1809 Lamarch & Lineages of Species don't go extinct ,but Change from one form to another; transformism 1809 ↳ Internal forces ↳ Inheritance of Characteristics.. Giraffes going for E extending · taller trees their neck over generations.. g , ↳ Continuous gradualChange. · George Cuvier & lar ge Curier & Catastrophism 1813 Catastrophism 1813. Added Linnaeus classification phyla to. Q Species gone extinct ; ② ↳ Catastrophic events e.. Floods. g ③ ↳ Biostratigraphy ; age of rocks & fossils. ⑪ 1) 1st Layer ; animals & plants fossils ; Lakes & Fresh water marshes. ⑤ 2) 2nd Layer (Sandstone) ; marine organisms. 3) 3rd Layer (gypsum limestone) ; freshwater species. 4) 4th Layer (coarse limestone) ; marine & freshwater Species. 5) 5th Layer (Chain , Sand , Clay) ; freshwater shels & driftwood. · Essentialism-Characteristics & behaviours inherently linked to genetics , not influenced by external factors. · Jean Baptiste Lamarch found Species do Change Overtime, Pass Changes to off Spring. George Cuvier found Species · have gone extinct , evidence supports this as fossils in rocus. · Charles Lyell proposes Earths Geological features Cause Catastrophic events. Volcanoes, Eg. Earthquakes. 1. 1 Brief History of Evolutionary Biology... -Charles Lyell & Uniformitarianism 1830 · Charles Lyell & Small Changes over time lead to state of earth. uniformitarianism 1830. Events line erosion & earthquakes are the same processes that have existed in the past. Charles Darwin & Natural Selection 1859 · Charles Dawin · Voyage on Beagle to Galapagos islands , & Natural Selection Forms better adapted to Survive will reproduce & pass on their fitness. 1859 · Evolution not inherently progressive. · No understanding of Genetics. Gregor Mendele Gregor Mendel & Heredity 1920. Heredity 1920 Hybridization of pea plants. · · Traits determined by heritible factors. Theory of her edity. · · Rafisher 1930 Modern Synthesislaa Sewall wright. · JBS Haldane · Merges Darwin Natural Selection & Mendells theory of Heredity. Sewell wright. Theoretical population genetics. Genetic Field research 1940 · Theodosius Dobzhanshy Theodosius Dobzhanshy - Evolution of Drosophila. · EB Ford 1940 EBFord - Natural Selection in moths. · HBD kette well HBD kettle well - melanism in moths. peppered Speciation - how one speciesSplits in two· Jean Baptiste Lamarack and Transformism; Species change over time and inheritance is acquired characteristics 1809...... - 1. 2 Evidence for evolution Artificial Selection- Evolutionary process which humans Specific trait in plants / Chose animals to pass future on to generations. Artificial Selection. Broccoli ; Selection for Suppression ↳ E of flower development g... Humans E g using Insecticides ↳ alleles resistants don't die ,. , insects with with pass them alleles to future generations. Seppered Moths Darker Stayed dirty moths due to the making buildings · alive air dark. Analogous Structures Analogous Structures - Features of different Species that haveSimilar functions but differentStructures , evolved independently to adapt to environment. ↳ Homologous Similarities are not explained by functional needs. Vestigial Structures Vestigial Structures - features of organism that are Considered to have lost their function through evolution. ↳ Appendix. ↳ Wisdom teeth. ↳ Goose bumps. Stop Codons do code for anything have been rejected from · not not evolution. , Can see divergence in lineages in fossil records. Artificial Selection- Evolutionary process which humans Specific trait in plants) Animals Chose to pass on to future generations. Analogous Structures - Features of different Species that haveSimilar functions but different Structures , evolved independently to adapt to environment. Vestigial Structures - features of organism that are Considered to have lost their function through evolution. 1. 3 Fossils & Geological Time Fossils Preserved plant & - animals whose remains have been buried. ↳ Soft parts decompose. ↳ Hard parts must be quickly buried. ↳ Very rare. · Amber; ancient treeSap Preserved insects. Mammotusfounda in frozen glaciers process of turning material lusually plant) into stone by infiltration without changing original Shape. Moulds & casts si · Sediment & minerals fill open Space Creating Cast Shaped like organism. Black = N white = R BioStratigraphy-uses fossils to establish relative ages of rock. Paleomagnetism-Study of earths magnetic field preserved in rocks. Geomagnetic reversal - Change in position of magnetic North & South. Fossils Preserved remains of plants & animals. Soft parts decompose hard parts , must be quickly buried Detrification-Process Where material is turned into Store by mineral infiltration , preserving original Shape. Molds & CaStS Formed Sediment fills space left by decomposed when organisms Creating a cast - , Dating techniques; BioStratigraphy Paleomagnetism , , geomagnetic reversal. 1. 3 Fossils & Geological Time AbsolutedatingRadiometriactive. isotopes a decay products in Sample. Half life amount of time it takes parent isotope to decay by into daughter - isotope. Make it into liquid, put it into Spectrometer and the isotopes. a a mass weigh Radiometric measures radioactive isotopes and decay products. Half life , time takes for parent isotope to decay into daughter isotope. Sample is liquidised , Analysed with mass Spectrometer to weigh isotopes.  1. 4 Paleoclimates peoples measurements , # wisitStudieda es ↳ Chemical proxies. ↳ Physical proxies. si ↳ Archives. Biological proxies Varve - Annual layer of Sediment. e Speleottems-mineral deposits that form in caves over time and record of past Climates Fossilised pollen fern spikes shows Stress. , · Tree rings. Ice cores ; snow accumulation -> glaciers. mical Proxies · 0' evaporates easier than O'8 During Ice age , Cooler temps extended to · equator. Heavy Oxygen Condenses out of atmosphere to lower latitudes than milder Conditions. Gives 018 longer to Condense So Current polar regions are more depletedin 018. · So le in current indicate extent of Ice Sheet former times cores polar regions in. Paleoclimates are studied Using Chemical , biological & physical proxies. Along with archives. Biological proxies-Varves , Spell others , fossilised pollen , tree rings , &Ice cores. Chemical proxies - Oxygen isotopes0 &08 Show temp patterns. lower 0. In leage , cooler temps Caused heavier Oxygen (08) toCondense , leavingecores with  1. 5 Natural Selection Natural Selection-Process which forms of organisms in a population that are best adopted increase in frequency Excess fecundity-Females produce more Offspring (eggs) than Survive. Adriation in population continuous Discrete · Height · Sex , · BodySize. Blood group. · Shin Colour. Attached earlobes. Eye colour. · Natural Selection Conditions Reproduction Individuals must be able to form a new generation -. Inheritance - Off SpringShould mostly look like parents. Variation - Individuals are not all identical. variation in fitness Some Characteristics increase reproducibility meaning more offspring -. Variation in populations Morphological cellular Biochemical DNA · Physical features. Number of Structures Sequence of · Sequence Of ofChromosomes. amino acids nucleotides within · Polymorphic ; more than proteins within gene. One recognisable form in Presence/absence a population. of genes & Proteins Natural Selection-process where traits that are best adapted to environment increases in frequency. Excess fecundity than organisms produce offspring can Survive - more. Types of population variation DNA Morphological · - - Cellular · Biochemical  Stabilising Selection-selecting from the mean & population Stabilises. Disruptive Selection - Favours the extremes. ① Directional Selection e.. g · Pink Salmon in Pacific NW has been decreasing inSize. ⑬ ⑬ Stabilising Selection eg. Human birth weight in W h.. A · 1935-1946 , babies with heavier or lighter birthweight were less likely to survive. ② DisruptiveSelection e. g. Q · African SeedCracker finch , Population exhibits 2 distinct beau Sizes , larged Small. · Birds with intermediate beak sizes are less efficient at eatingSmall or big Seeds. · Result; individuals with extreme traits have higher Survival & reproductive success. Types Selection of · Stabilising selection-favours mean & reduces variation. (human birth weight Directional Selection-favours one extreme , leading toShift. (Pacific Salmon Size decreasing). Disruptive selection favours both extremes over mean (African Seed cracker finch' beau Size). · -  1. 6 Coevolution Coevolution - where zor more species reciprocally effect each others evolution. Tetrodotoxin Story Rough Skinned NewtS toxin TTX · produce. ↳ helps protect them from predation. · Garter Snakes developed resistance to TTX. · More TTX production = More TTX resistance. Parasites & pathogens Red Queen Hypothesis · Natural Selection Operates on each Species to keep within improvements made by each Species. · Co evolution-species evolve in response to each other. Tetrodotoxin Story Newts produce - TTX , Garter Snakes evolve resistance. · Parasites & pathogens Hosts and parasites evolve in a of resistance & infectivity cycle -. · Red queen hypothesis - Species must continuously evolve to keep up with others. 2 1 Population. Genetics Hardy-Weinberg - Principle Stating that genetic variation in a population will remain Constant from one generation to the next. Gene frequency Proportion - each gene/ allele in population. Genotype-Genetic Combination of alleles found at given locus. Phenotype-Physical trait from given genotype that Can be observed. Homozygous dominant - AA Homozygous recessive - a a Heterozygous - Aa Assumptions of HardyWeinberg 1. No mutations. 2. Random mating.. No gene flow. 3 4. Very large population size.. No 5 natural selection. Equations Genotype Frequency Gene Frequency pi + 2pq + q2 = 1 P q + = 1 AA = P2 = P A = P Apa = P + QR a = 9 Me Me pi + 2pq + q2 = 1 P q + = 1 2 1 Population. Genetics... Example Observed genotype frequencies AA = 3/8 = 0. 375 P+ Q + R = 1 Aa = 3/8 = 0 375. 0 375 + 0 375 +.. 0. 25 = 1 aa = 2/8 = 0. 25 Example Observed allele frequencies (gene pool A= 109/140 = 0 779. P+ q = 1 a= 31/140 = 0 221. 0. 779 + 0. 221 = 1 Example Allele frequency p = p+ =Q q = R EQ + p = 0 4 +. z(0 3). q = 0 3+. z(0 3). P= 0 4 + 0.. 15 = 0. 55 9 = 0 3 + 0 15 = 0 45... P+ q= 1 0 55 +. 0. 45 = 1 2 2 Breaking Hardy Weinberg. Causes of Variation in a population Non-random Mating Can alter gene frequencies. Assortative mating-preference for similar genotypes/phenotypes. Disassortative for different mating-preference genotypes/phenotypes. Gene flow movement of individuals offspring population. · or in or out of a New organisms bring new alleles or different proportions of existing allele. Mutations · Impact of mutations between generations typically low. Natural Selection May take advantage. Natural Selection When one or more allele makes individual more fit. Mortality Selection - Certain genotypes survive better to reproduction. Fecundity Selection-Ability to produce More viable offspring than Others in a population. Modifying Hardy Weinberg Selection Coefficient (3) - Reductions in fitness (w) relative to the best genotype. S = 1 - w S must be between 0-1. Non random mating - Alters gene frequencies through assortative or disassortative. Gene Flow-Movement of individuals introduces new alleles, altering population allele frequencies. Mutations- frequencies selection Typically rare but can affect allele , natural may act on them. Natural Selection Certain improve fitness including mortality selection & alleles fecundity selection. - , 2 2 Breaking Hardy. Weinberg.... Fitness in Hardy Weinberg Mean Fitness = P2 (w1) + 2pq(wi) + q3(ws) w is the fitness for each genotype. Frequencies will not add up to 1. ↳ fix this by dividing each frequencies by mean fitness. Example Allele freguncies : Genotype Frequency Fitness (w) p = 0 36 + x0 48 = 0 6... P2 = AA 0. 36 1 q = 0 16. + X0 48 = 0 4.. 2pq = Aa 0 48. 1 q2 = aa 0. 16 0 8. ↑ D2 2pg ? q 0 36. 0. 48 0. 16 0 16 x 0 8.. Selection : 0 36. 0 48. 0 128. = 0. 968 - - L 0. 968 6 968. 0 968. = 0. 372 0. 496 0 132. = 1 p = p2 + pq = 0. 372 + 0. 496/2 = 0 62. 9 = P2 + p9 =0. 132 + 0. 496/2 = 0. 38 Mean Fitness = P2 (w1) + 2pq(wi) + q3(ws) 2 2 Breaking Hardy. Weinberg.... Calculating Allele Frequency Changes Xp = P frequencyo = Change in p -q = - p + Pi = Change in a frequency. w Xp = P frequencyo = Change in p -q = - p + Pi = Change in a frequency. w 2 3. variations in populations Mutation · Random Change of nucleotide. · Can bei ↳ Forward turning A into Crate a of u) ↳ Backward turning a into A Crate of V. P = - q = Example U = 8 6x10. 2 V = 4. 7X10 q= 1 -0 36. -Fo = = P P2x102 47x10 = 0. 13 NewMutationsmeanthatdeleterious alleemayneverleave a population i t Non Lethal = = Lethal = q = N Mutations ; Random Change of nucleotide. P = q = 2 3. variations in populations... Example Selection pressure - 0. 1 q = = = 0. 0 Inbreeding Mating of organisms more closely related than average relationship in population. Increases frequency of homozygous genotypes ; leading deleterious recessive · to allele. · Represented by F; ↳ probability that I alleles are identical by descent. ↳ The higher the F the , higher the effect of inbreeding + Fx = ( Example 4100ps = Fx = ()" " (i) 5)0 125 = =. Inbred Hardy-Weinberg homozygous dominant = P2 + PqF heterozygous Zpq-2pqF = homozygous recessive = q + pqF + Fx = (n  2 4 Genetic Drift. Genetic Drift-Random Changes in gene frequencies between generations. ↳ Directionless. · Rate of Change due to random drift depends on Size of population in Small greater ↳ populations. Predicting heterozygosity H= Heterozygosity of Current population. N = Number of individuals in population. At Aa ac 255025 H = (1 - )H = (- 05 = (1 - 0. 005)0 5. = 0. 4975 Genetic drift Founders effect-small group of individuals establish new , isolated population. Bottleneck effect-populations become periodically small. Migration Increases variation in a population. · Reproduction following migration prevents Speciation events. Genetic Drift-Random Changes in allele frequency between generations. Changes don't have Specific direction or purpose. - Rate is smaller populations. higher - in Heterozygosity - Measure of genetic variation within a population. 2 4 Genetic Drift.... Px = Px(1 M) + PyM - M Migration = rate proportion of population After migration immigrants in a -. Px = Allele frequency of the current population. Py = Allele frequency of the immigrant population. Bottleneck effect Occurs in declining population where the Surviving population is no longer representative of the original population, Founders effect - When new population is established by small group of individuals , reduces genetic variation. Bottleneck effect Population becomes periodically small , reducing genetic diversity. Migration - Introduces generic variation in a population. - Reproduction following migration Can prevent speciation. 3 1. What is a Species ? Species-group of organisms that can reproduce with each other & produce fertile offspring. Deme-local group of organisms that Share a gene pool & interbreed with each other. Cline-gradual Change in species biological traits across a geographical area. Vitamin B Folate Levels Clow) Increases risk of neural tube defects (e g arches.. of Spinal Chord fail to Close). Decreased Spermatogenesis (producing Sperm Cells). · Folate is essential for Synthesis of DNA in dividing cells. Vitamin D deficiency · Need to prevent reduction in folate levels , must be balanced with UV-B required for Vitamin D Synthesis. · Vitamin D enables Calcium absorption. · Deficiency leads to rickets. ↳ Richers ; bone disease bones in Children , weakened & deformed due to lack of Calcium , Vitamin D etc. Need to protectShin. Little need to protect Shin. Sufficient UV-B will penetrate Shin. Need to maximise UV-B3 Absorption to make to make Vit-D. Vit-D Species-group of organisms that can reproduce with each other & produce fertile offspring Deme-local group of organisms that Share a gene pool & interbreed with each other. Cline-gradual Change in species biological traits across a geographical area. Folate - essential for the Synthesis of new. DNA i needed to prevent reduction in folate levels. Vitamin 3 1. What is a Species ? Recognition Species Concept-group Of organisms that recognise each other as potential mates. Phylogenic Species Concept-Species according to which species is a lineage of populations between 2 phylogenetic branch points. Species Concepts Can be Vertical & Horizontal ; - Horizontal , define species at any given time point. -Vertical ; define Species throughout all time. Hybrid Speciation Formation of a brd Species from 2 Species that is reproductively isolated from both parental Species. Isolating barriers Habitat isolation - Reproductive isolation , two populations of a species are separated by different habitat even in same area. Temporal Isolation-Making or flowering times occur in different seasons. Behavioural Isolation-organisms have different Courting behaviours. Recognition Species Concept-group Of organisms that recognise each other as potential mates. Phylogenic Species Concept-Species according to which species is a lineage of populationsbetween 2 phylogenetic branch points. Hybrid Speciation - Formation of a 3rd Species from 2 Species that are reproductively isolated from both parental Species. 3 1. What is a Species ? Mechanical isolation-Physical differences prevents pollination or Mating. Gametic isolation - External fertilisation gametes are not attracted to each other &. Survive Hybrid Viability- Hybrid Zygotes have reduces viability or are inviable. Hybrid fertility-offspring of one or more Sexes fail to produce functional gametes. Hybrid breakdown Hybrids are infertile 3 2 Speciation. mechanisms zi Allopatry - Speciation classically comes from geographical separation. E. Kaibab Squirres g became geographically isolated from the Common Ancestor -. With it's Albert closest relative the Squirrel. 1 Peripatric Speciation - Founders effect , where new speciation forms from a small ↑ isolated population at the edge of a larger population. Sympatric Speciation -New Species evolve from existing Species Whilst Contining to X live in the same geographic area. E.. g Rhagoletus polomenella flies normally lay eggs on hawthorn fruits , started laying on apples. Can discriminate between · now apple & hawthorn races. Breeding times have now diverged to match fruit formation. Polyploidization Process by which an organism or cell acquires more than 2 complete Sets of chromosomes. Autopoly ploidy - When duplication of genomes occurs within a single species. · Allopolyploidy - When hybridisation& merging of genomes occurs between 2 species. si Parapatric Speciation-Species evolve into 2 subpopulations that are reproductively isolated from each other but Continue to exchange genes. Hybrid Species can form from this e Red wolf ·. g.. Reinforcement-consolidation of a derived trait in order to be maintained in a Population. ButterfliesChoosing E g. males with Similar markings. Polyploidization-organism or cell acquires more than 2 complete sets of chromosomes. ↳ Autopolyploidy - When duplication of genomes occur within a single species. ↳ Allopolyploidy - when hybridisation & merging of genome occurs between 2 species..3 3 Molecular Clocks Physical Changes are caused by mutations at a molecular level E g Adenine-Guanine... Mutations Caused internally or externally. · Internal errors caused by errors in DNA replication & through errors that aren't repaired. · Types of mutations : TGACTA - Substitution. TGCCCTA - Insertion. TGCTA-Deletion TGCATC - Inversion. Molecular Clock-Theory that States that DNA protein sequences evolve at a rate that is constant over time. Genetic differences between any 2 Species is proportional to the time Since they Share a Common ancestor. Calibrations with known fossil records Finding a fossil : Marks the earliest know appearance of a particular group of organisms. Gives a point in time when the Species Split apart. · Comparing DNA : Scientists compare DNA Sequences , counting number of mutations between their DNA Sequence · Mutation rate : Mutation rate = NO DNA. Changes Fossils age.0 E g = Imutations /mil. yearsh Molecular Clocks - Theory that States DNA protein Synthesis evolve at rate that is Constant over time. Mutations : Caused internally or externally. Change in DNA Sequence.3 3 Molecular Clocks... Phylogenetic Relationships (molecular Clock). Compare DNA Sequences from different species to see how similar/different they are · Molecular Clocks put dates on the branches of trees - genetic differences between species using ↳ By Counting the number of mutation rates , Can estimate when branches Split.. If species have 3E few from Common. g differences in their DNA , likelyhave Split ancestor relatively recently. Neutral Theory of Evolution · Proposes that most mutations , especially amino acids, are not strongly beneficial or harmfull , they're effectively neutral. Due to : Having very little effect the organisms fitness. · on · Doesn't significantly improve or reduce function of proteins. These don't have a major effect because : · Some DNA mutations result in amino acids that have similar Chemical properties , not dramatically altering proteins Shape / function. Population Size & Molecular Clocks · Species with long generation times tend to have smaller population Sizes. Nearly ↳ Neutral mutations' · Small populations : Random drift. · Larger populations : Selection. Relaxed molecular clock · Rate varies over time among organisms Evolutionary rate evolves overtime because rate of molecular evolution is led to other biological · Characteristics. · Molecular (locks estimate evolutionary time by Comparing DNA Sequences & mutation rates. · Neutral mutations , which don't affect fitness , are key to neutral theory of evolution. Population Size impacts Molecular Clocks ; Smaller populations experience random drift , whilst larger ones are shaped by Selection. Relaxed for · molecular clocks account variations in mutation rates across species. · Evolutionary rales are linked to biological & species - Specific factors.  3. 4 Artificial Selection Humans Consciously Select for against particular features in · or an organism. Benefits & Risks Benefits Risks New varieties that are economically Reduced genetic variation Can lead to increases in important. homozygous diseases. Better quality/quantity of food. · Rare disease genes unknowingly selected for as Selection against harmful traits. part of a positive trait. · Physical problems in organism. Genetic Engineering ① Agrobacterium : has ability to transfer DNA into plants. used to introduce new genes to plants. ②DNA modification : Targeted DNA Segments in Agro genome is removed. In it's place, new recombinant DNA fragments with desirable traits e g. tolerant. to herbicides. ③ Culturing modified agrobacterium : Cultured to make large population of bacteria Carrying new genetic material. Injecting plant : Modified agro injected into plant , bacterium transfers recombinant DNA into plants genome , introducing new traits. ⑤ Breeding modified plant : After plant successfully integrates new DNA, displays modified traits Can. then be bred to plants Characteristics. produce more with Same Artificial Selection-Humans Select Specific traits in organisms to enhance or Suppress. Genetic Engineering -- Agrobacterium transfers DNA into plants. Targetted DNA modification introduces desirable traits. Modified bacterium Cultured to produce genetic material ·. · plantsinjectedwith modified bacteriadisplay new trita 3. 4 Artificial Selection... Genetic engineering of Insulin 1 ①Gene that codes for insulin is extracted from DNA 3 4 5 Of normal human cell using enzyme. ②plasmid isolated from bacterium & human insulin gene is 2 inserted. ③ Plasmid Vector is inserted into bacterium. ⑪ Bacteria reproduces , creating new bacteria that all have the plasmid Vector & produceinsulin. ⑤ Insulin Can be extracted & used to treat people with diabetes. Conventional breeding & Genetic Modification Conventional breeding two plants with desirable traits are cross pollinated to Combine traits. This ↳ mixes genetic material through natural reproduction. Slow process requiring many , generations. Genetic modification · Specific genes are isolated. Using genetic engineering genes , are inserted directly into targets plants genome. · Produced plant in a single step Saving, time. Genetical Engineered Insulin-Isolates human insulin gene , insert into bacterial plasmids transform bacteria , , Culture bacteria insulin , purify. Conventional breeding-Mixes genetic material of z plants with desirable traits , Slow process. Genetic modification-Genes inserted directly into targets plant genome , Produces in Single trait. 4 1 Human. Evolution Hominidae-Super family which includes all living & extinct ape & human species. Hominin-General term for humans a human line ancestors. Sagittal crest-prominent ridge of bone. Attach temporalis muscle. Ardipithecus-Human & Chimpanzees diverged between 7-4MYA. Evolution of genus Homo Homo habilis Earliest representative of genus Homo 2 8 · mya..