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Evolution Evolution BASIC: change over time BIOLOGY: change in the gene frequency of a population over time - individuals do not evolve - changes in the population accumulate and eventually lead to change TYPES of Evolution Microevolution: change in the gene pool (genetic content) of a population EX: normal variations Macroevolution: change on a large scale leading to new and different species EARLY THEORIES CONTRIBUTING TO DARWIN Hutton: gradualism - slow happenings of geology Lyell - geologist - uniformitarianism - geological systems are constant Lamark: inheritance of acquired traits and use and disuse - individuals acquired traits would be passed down to the next generation - USE AND DISUSE EX: giraffe blacksmith - disproved: mice and tails Linnaeus (classification) Hutton (gradual geologic change) Lamarck (species can change) Malthus (population limits) Cuvier (fossils, extinction) Lyell (modern geology) Darwin (evolution, natural selection) Mendel (inheritance) American Revolution 1750 Wallace (evolution, natural selection) French Revolution U.S. Civil War 1800 1850 1900 1795 Hutton proposes his theory of gradualism. 1798 Malthus publishes “Essay on the Principle of Population.” 1809 Lamarck publishes his theory of evolution. 1830 Lyell publishes Principles of Geology. 1831–1836 Darwin travels around the world on HMS Beagle. 1837 Darwin begins his notebooks on the origin of species. 1844 Darwin writes his essay on the origin of species. 1858 Wallace sends his theory to Darwin. 1859 The Origin of Species is published. 1865 Mendel publishes inheritance papers. Figure 22.2 DARWIN - HMS Beagle & Galapagos - collected different species - noticed similarities to other species on other islands and South American species CONCLUSION: new species could arise from an ancestral form by the gradual accumulation of adaptations to a different environment DESCENT WITH MODIFICATION CLASSIC: FINCHES - big beaks and little beaks - big seeds in dry - little seeds when wet Driving force: Natural Selection and Adaptation (survival of the fittest) - those that survive get to breed and pass on their traits POINTS of Natural Selection 1. great potential for reproduction 2. populations remain stable in size 3. resources are limited in size RESULT: competition for resorces 4. variation in population 5. variation mostly due to genetic recombination and inheritance RESULT: survival dependent on better suited characteristics RESULT: better characteristics get passed on to next generation THUS: Organisms are “shaped” into those that best fit the environment ARTIFICIAL SELECTION: analogous evidence choose traits and breed them - in the wild? Artificial selected traits revert back to wild type Terminal bud Lateral buds Brussels sprouts Cabbage Flower cluster Leaves Cauliflower Kale Flower and stems Broccoli Stem Wild mustard Figure 22.10 Kohlrabi KEY POINTS: only populations evolve - cumulative change over a period of time only heritable traits are amplified or diminished Evidence for Evolution Keep in Mind: Theory and logic are not the same as evidence. Real evidence only has one interpretation Not all Truth is Factual. “Truth takes time.” – Irina Derevko EVIDENCE OF EVOLUTION 1. Biogeography - species of nearby areas populate those around it - evolution of a species is going to be based on what was near it EX: South American species are going to be more like North American than Australian Evidence: Fossil record - present day species should have fossils of other things like them PROBLEMS: - fossil record - HUGE GAPS 2. Comparative Anatomy: -species that evolved from a common ancestor should have similar anatomical structures HOMOLOGOUS STRUCTURES: - same components but different variations Vestigial Organs: remainders of past use Homologous Structures Human Figure 22.14 Cat Whale Bat 3. Comparative Embryology: “ontogeny recapitulates phylogeny” ontogeny = development phylogeny = past history - means as the individual develops embryological, the embryo shows the past history or evolution of the species EX: gill slits on human embryo PROBLEM: embryological studies show some of the greatest differences between species Comparative embryology Pharyngeal pouches Post-anal tail Chick embryo Figure 22.15 Human embryo 4. Molecular Biology - comparison of DNA, RNA and proteins from species to see similarities – closer the molecule, the closer the relation - Cytochrome C - cellular respiration - very similar - all from one original source variations due to mutations Microevolution: STUDY OF MICROEVOLUTION = POPULATION GENETICS - study of genetic variation in a population and how it changes from one generation to another Uses a MODERN SYNTHESIS approach - studies populations as the units of evolution (not individuals) using principles from different fields of study POPULATION: localized group belonging to one species SPECIES: group of populations whose individuals have the potential to interbreed and produce viable (fertile) offspring Study of Population focus: GENE POOL = total aggregate of genes in the population Generation 1 CW CW genotype CRCR genotype Plants mate Generation 2 All CRCW (all pink flowers) 50% CR gametes 50% CW gametes Come together at random Generation 3 25% CRCR 50% CRCW 50% CR gametes 25% CWCW 50% CW gametes Come together at random Generation 4 25% CRCR 50% CRCW 25% CWCW Alleles segregate, and subsequent generations also have three types of flowers in the same proportions Analyzed using HARDY WEINBERG EQUATION - focuses on frequencies of alleles AND genotypes = genetic structure - tells us if a population is evolving or not - if there is NOT change in the frequencies = NOT evolving - if there IS change in the frequencies = Evolving PRINCIPLES OF HARDY WEINBERG THEORUM: - genetic frequencies of a population remain the same unless acted on by an outside force = HARDY WEINBERG EQUILIBRIUM - reshuffling of alleles through reproduction has no affect on frequencies UNDER SPECIFIC CONDITIONS USE HW Equation p2 + 2pq + q2 = 1 - represents the possible combinations and percent probabilities of crosses derived from p + q = 1 (amount of dominant + amount of recessive = 100%) - why squared? how do you get homozygous dominant? Punnet square: Aa X Aa - one way to get AA = 1/2 from father , 1/2 from mother = 1/4 - aa = same - heterozygous: Aa or aA - 2 ways = percent probability x 2 p = dominant allele q = recessive Gametes for each generation are drawn at random from the gene pool of the previous generation: 80% CR (p = 0.8) 20% CW (q = 0.2) Sperm CR (80%) CW (20%) p2 Eggs CR (80%) pq p2 16% CRCW (20%) CW 64% CRCR 16% CRCW qp 4% CW CW q2 If the gametes come together at random, the genotype frequencies of this generation are in Hardy-Weinberg equilibrium: 64% CRCR, 32% CRCW, and 4% CWCW Gametes of the next generation: 64% CR from CRCR homozygotes + 16% CR from CRCW homozygotes = 80% CR = 0.8 = p 4% CW from CWCW homozygotes + 16% CW from CRCW heterozygotes = 20% CW = 0.2 = q With random mating, these gametes will result in the same mix of plants in the next generation: Figure 23.5 64% CRCR, 32% CRCW and 4% CWCW plants Calculating the Frequency of a Gene # of a Specific Allele/Total # of all Alleles 320 AA 160 Aa and 20 aa Frequency of A = (640 + 160)/1000 Frequency of a = (160 + 40)/1000 WHY 160 for each? heterozygous WHAT IF YOU ARE DOING A FIELD STUDY? can’t tell homozygous dominant from a heterozygous use the frequency of the homozygous recessive to calculate probabilities 1. TAKE recessive phenotype ex. 20 out of 500 = 0.04 = 4% - represents frequency of q2 2. TAKE square root = .2 3. use p + q = 1 equation to solve for p p=1-q p = 0.8 4. Plug frequencies of p and q into HW equation and solve. WHEN DOES THIS APPLY? - study of a population for one generation - study of next generation will show if the population is evolving - if change = evolution CAUSES OF MICROEVOLUTION/REQUIREMENTS FOR HW - the causes of microevolution are the opposite for the requirements for HW to be maintained MICROEVOLUTION 1. GENETIC DRIFT - change in the gene pool due to chance - smaller sample of individuals Specific Types of Genetic Drift: Bottle Neck Effect - natural catastrophe reduces population to a few individuals - become parents of resulting population - can wipe out a certain trait Founder Effect - a few individuals start the population HW 1. Very large population - allows for greater mixing CWCW CRCR CRCR Only 5 of 10 plants leave offspring CRCW CWCW CRCR CRCR CRCW CWCW CRCR CRCW CRCW CRCR CWCW CRCW CRCR CRCR CRCW Generation 1 p (frequency of CR) = 0.7 q (frequency of CW) = 0.3 Only 2 of 10 plants leave offspring CRCR CRCR CRCR CRCR CRCR CRCR CRCR CRCR CRCW CRCW Generation 2 p = 0.5 q = 0.5 Figure 23.7 CRCR CRCR Generation 3 p = 1.0 q = 0.0 (a) Shaking just a few marbles through the narrow neck of a bottle is analogous to a drastic reduction in the size of a population after some environmental disaster. By chance, blue marbles are over-represented in the new population and gold marbles are absent. Figure 23.8 A MICROEVOLUTION 2. Gene Flow individuals move in or out of the population introducing or removing new alleles HW 2. ISOLATION from population - no gain or loss of genes MICROEVOLUTION 3. Mutations - introduce new alleles - rare - most are fatal or have no effect 3. No mutations HW MICROEVOLUTION 4. Non-random matingmost animals choose based on some characteristic - isolates favorable traits Types: Selective – specific trait is favored inbreeding - closely related assortive mating - similar phenotype HW 4. Random mating - all traits treated equally MICROEVOLUTION 5. Natural Selection - best fit survive HW 5. No natural selection - all equal chance of survival MICROEVOLUTION AND VARIATION MICROEVOLUTION IS DEPENDENT ON GENETIC VARIATION Interspecies Variation 1. Quantitative: polygenic inheritance - continuum of characteristics EX height 2. Discrete: either/or trait may be two traits or more - if more = POLYMORPHISM Interpopulace variation (geographic variation) Altitude Latitude Proximity of Other Species: - mutualism - predator - competition Heights of yarrow plants grown in common garden EXPERIMENT Researchers observed that the average size Mean height (cm) of yarrow plants (Achillea) growing on the slopes of the Sierra Nevada mountains gradually decreases with increasing elevation. To eliminate the effect of environmental differences at different elevations, researchers collected seeds from various altitudes and planted them in a common garden. They then measured the heights of the resulting plants. Atitude (m) RESULTS The average plant sizes in the common garden were inversely correlated with the altitudes at which the seeds were collected, although the height differences were less than in the plants’ natural environments. CONCLUSION The lesser but still measurable clinal variation in yarrow plants grown at a common elevation demonstrates the role of genetic as well as environmental differences. Figure 23.11 Sierra Nevada Range Great Basin Plateau Seed collection sites GENERATION OF VARIATION: 1. Mutation - change in the DNA - rare - mostly harmful - only those that matter rate: 1 mutation per 100,000 genes per generation 1/1000chance – 99% lethal - must be heritable - role of mutagens impact: page 437 2. sexual recombination - shuffles the genes Preserving Variation - without variation, populations are more susceptible to disease Preserving Variation; 1. Sexual Reproduction vs. Asexual 2. Diploidy - one trait masks another - mutation = lead to recessive defect Dominance due to diploidy cancels defect 3. Balanced Polymorphism - Maintaining a variety of traits - allows for survival of species - Ex: finches and beak size 4. Heterozygote advantage: heterozygote better survivor maintains all frequencies EX: sickle cell anemia 5. Hybrid vigor: mixing of traits produces stronger better plant 6. Frequency-dependent polymorphism- one trait is not necessarily better - once its frequency gets 2 high , it drops 7. Sexual Dimorphism: difference in males and females choosing a mate based of different physical characteristics: - may connote fertility - protective - strength TYPES OF NATURAL SELECTION - compare three types of individuals two extremes and middle ground correlate to polygenic trait Stabilizing Selection: favors middle ground - bird beaks – human birth weight and size Directional Selection: favors an extreme - giraffe Diversifying Selection: does not favor middle ground makes both extremes more frequent - snails and shell color Original population Original population Evolved population (a) Directional selection shifts the overall makeup of the population by favoring variants at one extreme of the distribution. In this case, darker mice are favored because they live among dark rocks and a darker fur color conceals them from predators. Fig 23.12 A–C Phenotypes (fur color) (b) Disruptive selection favors variants at both ends of the distribution. These mice have colonized a patchy habitat made up of light and dark rocks, with the result that mice of an intermediate color are at a disadvantage. (c) Stabilizing selection removes extreme variants from the population and preserves intermediate types. If the environment consists of rocks of an intermediate color, both light and dark mice will be selected against. NATURAL SELECTION: movement toward perfection? 1. historical constraints 2. compromises 3. non-adaptive evolution 4. can only work with what’s present BIOLOGICAL SPECIES CONCEPT Species = group of populations whose members have the potential to interbreed with one another in nature to produce viable, fertile offspring, but who cannot produce viable, fertile offspring with members of others species Qualifications: - natural environment -may not take into account morphological differences - wolf, dog and coyote - does not apply to species that do not reproduce sexually - does not explain gene flow between separate species SPECIATION: formation of a new species Modes of Speciation Anagenesis – one species changing into a different type – original is gone Cladogenesis – one species diverting into two or more with the original still present – “branching” Figure 24.2 (a) Anagenesis (b) Cladogenesis Species Barriers TWO BASIC TYPES: prezygotic (prevent fertilization) and postzygotic (prevent hybrid from being fertile or reproductively successful) PREZYGOTIC BARRIERS 1. Habitat Isolation: different places - can’t breed 2. Behavioral Isolation: different courtship behaviors different mate attractions - fireflies 3. Temporal (time) Isolation: breed during different times - skunks - flowers 4. Mechanical Isolation: physically can’t breed “anatomically incompatible” 5. Gametic Isolation: gametes can’t fuse - female’s reproductive tract may be inhospitable to foreign sperm sperm can’t fuse to egg biochemical signals - recognition proteins on surface of the egg allow sperm to fuse Prezygotic barriers impede mating or hinder fertilization if mating does occur Habitat isolation Behavioral isolation Temporal isolation Individuals of different species Mechanical isolation Mating attempt HABITAT ISOLATION TEMPORAL ISOLATION BEHAVIORAL ISOLATION (b) MECHANICAL ISOLATION (g) (d) (e) (f) (a) (c) Figure 24.4 POSTZYGOTIC BARRIERS 1. Reduced Hybrid Viability - embryo fails to develop - very weak offspring - die 2. Reduced Hybrid Fertility - sterile: Mule (male donkey + female horse) or Hinny (female donkey + male horse – less successful) male mules are sterile, females can sometimes back breed with donkey or mule - usually can’t back breed with parent species 3. Hybrid Breakdown - reproduce for one generation Gametic isolation Reduce hybrid fertility Reduce hybrid viability Hybrid breakdown Viable fertile offspring Fertilization REDUCED HYBRID VIABILITY GAMETIC ISOLATION REDUCED HYBRID FERTILITY HYBRID BREAKDOWN (k) (j) (m) (l) (h) (i) MODES OF SPECIATION: how species are formed ALLOPATRIC (physical isolation) vs. SYMPATRIC (intrinsic - change of genetic info) Figure 24.5 A, B (a) Allopatric speciation. A (b) Sympatric speciation. A small population becomes a new species population forms a new species while geographically without geographic separation. isolated from its parent population. ALLOPATRIC: 1. Geographical barriers - two groups get separated into different areas - genetic drift - natural selection leads to genetic differences - geographical barrier may a difference of niche causes natural selection in one area that does not occur in another 2.Isolation of a small group (founder effect) 3. Peripheral Isolate - favors natural selection and genetic drift 3. Adaptive Radiation: species jumping from one island to another - each time new group or colony grows may lead to natural selection or genetic drift - all from a common ancestor SYMPATRIC SPECIATION: genetic isolation within the parent species TYPES: PLANT polyploidism - more than diploid - faulty cell division that results in extra sets of chromosomes 1. AUTOPOLYPLOID: polyploidism - all chromosomes from the same species - in plants: can result in VIGOR - better and stronger traits - results in a new species if the polyploidism is an even set of chromosomes (4N) and there is self-fertilization - can’t interbreed with normal parent species = 2n 2. ALLOPOLYPLOID: polyploidism - chromosome sets from different species - interbreeding = combined chromosomes - usually sterile (odd numbers of chromosomes in gametes) - can reproduce asexually - Failure of cell division in a cell of a growing diploid plant after chromosome duplication gives rise to a tetraploid branch or other tissue. Gametes produced by flowers on this branch will be diploid. Offspring with tetraploid karyotypes may be viable and fertile—a new biological species. 2n 2n = 6 4n = 12 Figure 24.8 4n Unreduced gamete with 4 chromosomes Hybrid with 7 chromosomes Species A 2n = 4 Unreduced gamete with 7 chromosomes Viable fertile hybrid (allopolyploid) Meiotic error; chromosome number not reduced from 2n to n 2n = 10 Normal gamete n=3 Species B 2n = 6 Figure 24.9 Normal gamete n=3 ANIMAL: 1. reproductive isolation - dependent on specific resources - wasps and figs: specific figs - specific wasps 2. natural selection 3. mutation GENETIC CHANGE CAN LEAD TO SPECIATION - different environments = natural selection = speciation - reproductive isolation results as a secondary effect HOW MUCH CHANGE IS ENOUGH? various - depends on what is changed TEMPO OF CHANGE: gradualism vs. punctuated equilibrium gradualism = very small changes over a period of time - not supported by fossil record FOSSIL RECORD: - shows stasis - no change for long periods of time then disappear - replaced by something different - little to no transition POSSIBLE EXPLAINATION: changes that occurred are not seen in the fossils because they were in the soft tissues or were behavioral -PUNCTUATED EQUILIBRIUM - stayed same for long periods of time and then underwent periods of rapid change for some reason (presumably change in the environment) - does not allow enough time for fossils to be formed so there are none Figure 24.13 Time (a) Gradualism model. Species (b) Punctuated equilibrium descended from a common model. A new species ancestor gradually diverge changes most as it buds more and more in their from a parent species and morphology as they acquire then changes little for the unique adaptations. rest of its existence. Possible mechanisms for Punctuated Equilibrium 1. polyploidy = only plants = still similar 2. exaption and natural selection: plasticity of traits - can be used for one thing or another - may then give selective advantage and lead to development of a different trait EX: reptiles into birds 3. change in control genes of development (Homeotic Genes) - in embryology: genes activate other genes (cascading effect) that direct development - mutation here could result in change of development EX: allometric growth - how the body grows - arms grow before legs - change could result in a different trait or ability Fig. 2 Representative skeletal phenotypes of newborns of the Hoxa13;Hoxd11-13;Gli3 allelic series. Rushikesh Sheth et al. Science 2012;338:1476-1480 Published by AAAS Fig. 1 (A) Expression of Sox9 in E12.5 limbs of the Hoxa13;Gli3 allelic series. Rushikesh Sheth et al. Science 2012;338:1476-1480 Published by AAAS Fig. 5 Vertebrate limb evolution and distal Hox gene function. Rushikesh Sheth et al. Science 2012;338:1476-1480 Published by AAAS 4. Chronology of development: time for development to occur ex. humans and chimps - humans brains grow for longer periods of time - prolonged juvenile characteristic Phylogenic Systematics PHYLOGENIC - evolutionary history SYSTEMATICS - study of biological diversity in evolutionary context - study of biological diversity using evolutionary history Basis of Phylogenic Studies Geology and the Fossil Record Formation of Fossils - stratification of earth - oldest layers at bottom of strata - sedimentation - animals/plants die - become part of strata 1 Rivers carry sediment to the ocean. Sedimentary rock layers containing fossils form on the ocean floor. 2 Over time, new strata are deposited, containing fossils from each time period. 3 As sea levels change and the seafloor is pushed upward, sedimentary rocks are exposed. Erosion reveals strata and fossils. Younger stratum with more recent fossils Older stratum with older fossils Types of Fossils - hard parts of organisms remain - organic substances replaced with mineral - organic substance decays - leaves space - cast - preservation of organic - pressed between layers and kept from air - no decomposition by bacteria or fungi - amber - ice (c) Leaf fossil, about 40 million years old (b) Petrified tree in Arizona, about 190 million years old (a) Dinosaur bones being excavated from sandstone (d) Casts of ammonites, about 375 million years old (f) Insects preserved whole in amber Figure 25.4a–g (g) Tusks of a 23,000-year-old mammoth, frozen whole in Siberian ice (e) Boy standing in a 150-million-year-old dinosaur track in Colorado Dating Fossils - relative vs. absolute RELATIVE - geologic time scale - older, younger, after, before - based on strata in rock - different layers – ERAS of SIGNIFICANCE - Cambrian - explosion of animals Absolute Dating - not “errorless” - given in years RADIOMETRIC DATING: - Half-Life - time it takes for half the atoms in a radioactive sample to decay into a more stable atom - measure the amount of isotopes in a fossil and work backwards EX: Carbon 14 - half life - 5600 -dating: look at amount of carbon 14 in a sample and move backwards - use larger half-lives of different compounds to date older specimens Ratio of parent isotope to daughter isotope Accumulating “daughter” isotope 1 2 Remaining “parent” isotope 1 14 18 2 Time (half-lives) 3 1 16 4 - Racemization: conversion of amino acids from biological form (L) to non-biological (D) (enantiomers) - biological systems only make L - convert to D - not accurate - rate changes with temperature GEOLOGY AFFECTING PHYLOGENY CONTINENTAL DRIFT - PANGEA - plate tectonics - shifting of plates - bring together and separate species geographically Phylogenic Patterns - adaptation and radiation - major catastrophe = mass extinction - sudden changes = more adaptation = more speciation - ADAPTIVE ZONE - set of new living conditions and resources that presents new possibilities Mass Extinction - trace mass extinctions using fossil record - - when lots die - leave more fossils - if extinct don’t show up in the next layers Predation loss of habitat Volcanoes global warming Meteors - impact hypothesis Use of Phylogenic Information - develop PHYLOGENIC TREES - diagram to trace evolutionary relationships AS BEST AS THEY CAN BE DETERMINED - relate species based on common characteristics basis of TAXONOMY = classification Taxonomic Hierarchy Hierarchy: Each level = taxon - classification level Domain - largest grouping Kingdom Phylum Class Order Family Genus Species- smallest grouping - subspecies - variety Scientific Names Scientific Name = Genus species Binomial - two names “species” - specific epithet Domain Eukarya Kingdom Animalia Phylum Chordata Subphylum Vertebrata Class Mammalia Order Carnivora Suborder Caniformia Family Canidae Species Canis lupus Subspecies Canis lupus familiaris As you classify an organism you make a PHYLOGENIC TREE - shows the taxonomic hierarchy - each branch is a taxon Bacteria, Oak, Amoeba, Starfish, Fish, Horse, Wolf, Dog Taxonomic Trees usually represent Phylogenic Trees - shows evolutionary trends - closer they are on the tree = closer evolutionary history Cladograms Cladogram: depiction of patterns of shared characteristics among taxa Clade: group of species that includes an ancestral species and all its descendants Cladistics: the study of resemblances among clades Species Genus Panthera Order Family Panthera Mephitis Canis Canis Lutra lutra pardus mephitis familiaris lupus (European (leopard) (striped skunk) (domestic dog) (wolf) otter) Felidae Mephitis Lutra Mustelidae Carnivora Canis Canidae TYPES OF PHYLOGENIC BRANCHES 1. Monophyletic: all descendents from a common ancestor E D J H G F C K I B A (a) Monophyletic. In this tree, grouping 1, consisting of the seven species B–H, is a monophyletic group, or clade. A monophyletic group is made up of an ancestral species (species B in this case) and all of its descendant species. Only monophyletic groups qualify as legitimate taxa derived from cladistics. 2. Polyphyletic: same taxon, but different ancestors D E G J H I F C K B A (c) Polyphyletic. Grouping 3 also fails the cladistic test. It is polyphyletic, which means that it lacks the common ancestor of (A) the species in the group. Furthermore, a valid taxon that includes the extant species G, H, J, and K would necessarily also contain D and E, which are also descended from A. 3. Paraphyletic: separate branch G E D C J H K I F B A (b) Paraphyletic. Grouping 2 does not meet the cladistic criterion: It is paraphyletic, which means that it consists of an ancestor (A in this case) and some, but not all, of that ancestor’s descendants. (Grouping 2 includes the descendants I, J, and K, but excludes B–H, which also descended from A.) all based on comparative science HOWEVER: may have similarities and not really be related - analogous structures - look / function the same - different lineage - differs from homologous structures - different form, same lineage FINDING PHYLOGENIC RELATIONSHIPS 1. Comparative anatomy 2. Molecular biology a. protein comparison amino acid sequences compared - similar sequence = similar gene = common ancestor - more similar = more closely related = more recent divergence on tree Human Human Mushroom 0 Mushroom Tulip 30% 0 Tulip (a) Percentage differences between sequences 40% 40% 0 25% 15% 15% 15% 20% 10% 5% 5% Tree 1: More likely (b) Comparison of possible trees Tree 2: Less likely b. DNA and RNA comparison DNA-DNA hybridization - take single strand of DNA from one species and a single strand from another - put together - amount of similarity will determine how closely two species are related Restriction Maps: - restriction enzymes, electrophoresis - compare bands of species - more similar = more related - usually compare mitochondrial DNA (mtDNA) DNA Sequence Analysis: -compare actual nucleotide sequences - use rRNA - little change Lamprey Tuna Turtle Leopard Salamander Lancelet (outgroup) CHARACTERS TAXA Hair 0 0 0 0 0 1 Amniotic (shelled) egg 0 0 0 0 1 1 Four walking legs 0 0 0 1 1 1 Hinged jaws 0 0 1 1 1 1 Vertebral column (backbone) 0 1 1 1 1 1 Turtle (a) Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present. Leopard Hair Salamander Amniotic egg Tuna Four walking legs Lamprey Hinged jaws Lancelet (outgroup) Vertebral column (b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny. Cladograms Follow the rule of Maximum Parsimony – simplest is best Plesiomorphic Traits – common in all branches – can’t be used to make a new clade Apomorphic Traits – derived, novel, new traits - form a new clade Synapomorphic Traits – shared, derived trait in clades (common branch) Apomorphy for tetrapods Plesiomophy for vertebrates How to Make a Cladogram How to #2 MAJOR LINEAGES OF LIFE: Original: Plants and Animals Plants, animals, fungi Plant, animals, fungi, bacteria TRADITIONAL FIVE KINGDOM APPROACH P, A, F, Protista, Monerans Splitting of Groups based on biochemical information Eight Kingdom Approach split the monerans based on metabolism Bacteria Archaea - old bacteria split protista into three groups based on structure and feeding methods THREE DOMAIN APPROACH - isolates bacteria, archae and eukarya into separate groups - emphasizes evolutionary relationships and biochemical differences - further fragments protista based on feeding and structure Figure 26.22 Domain Archaea Universal ancestor Domain Eukarya Domain Bacteria Figure 26.21 Plants Fungi Animals Bilaterally symmetrical animals (annelids, arthropods, molluscs, echinoderms, vertebrates) Cnidarians (jellies, coral) Sponges Choanoflagellates Club fungi Sac fungi Arbuscular mycorrhizal fungi Zygote fungi Chytrids Amoebozoans (amoebas, slime molds) Angiosperms Gymnosperms Seedless vascular plants (ferns) Bryophytes (mosses, liverworts, hornworts) Charophyceans Chlorophytes Red algae Cercozoans, radiolarians Stramenopiles (water molds, diatoms, golden algae, brown algae) Alveolates (dinoflagellates, apicomplexans, ciliates) Euglenozoans Diplomonads, parabasalids Euryarchaeotes, crenarchaeotes, nanoarchaeotes Korarchaeotes Gram-positive bacteria Cyanobacteria Spirochetes Chlamydias Proteobacteria 3 Domains PREBIOTIC EVOLUTION "This chapter is the most speculative of the unit, for its main subject is the origin of life on a young Earth, and no fossil record of that seminal episode exists." - Campbell, page 490, 5th Edition Origin of Life Formation of the earth THE YOUNG EARTH - little atmospheric oxygen - high UV - lightning - volcanoes - conducive to chemical reactions - energy - no oxygen to oxidize products and break them down Hot mixture of chemicals - formed amino acids and nucleic acids - formed proteins, RNA, and DNA - formed simple cells (Protobionts) - formation of heredity - cells became more complicated Glucose-phosphate 20 m Glucose-phosphate Phosphorylase Starch Amylase Phosphate Maltose Maltose (a) Simple reproduction. This liposome is “giving birth” to smaller liposomes (LM). (b) Simple metabolism. If enzymes—in this case, phosphorylase and amylase—are included in the solution from which the droplets self-assemble, some liposomes can carry out simple metabolic reactions and export the products. Miller/Urey Experiment - simulated primitive earth using the information from their time travel experiment where they actually went back in time and determined what the earth was like - methane, water, ammonia, H2, and electricity - excluded CO, CO2, N2 and O2 FOUND: produced amino acids change components and even produce all amino acids, nucleotides and ATP ABIOTIC FORMATION OF PROTEINS - in labs = Yes - control - concentrated - role of clay - catalyze synthesis Formation of Simple Cells = PROTOBIONTS - aggregates of abiotically reproduced molecules - separate internal environments - may have metabolic activity if an enzyme is present - may aggregate – “grow” and split - like oil drops Formation of Nucleic Acids - abiotic generation of nucleotides - self assemble - self replicate - require a lot of nucleotides (concentration) - RNA can act as ribozyme to catalyze reactions - build proteins - build other RNAs - each could change and have a molecular selective advantage - then ….