BIOA01 FINAL EXAM NOTES

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Department
Biological Sciences
Course
BIOA01H3
Professor
Mark Fitzpatrick
Semester
Fall

Description
BIOA01 Exam Notes MICROEVOLUTION- LEC 25  Bio Evolution: change in allele frequencies in populations over time o individuals are not evolving, over generations  Microevolution: changes within a species, by natural selection o Evolution requires heritable changes in DNA to be passed down generations  Macroevolution: changes between different species  4 Major forces of evolution: mutation, genetic drift, migration, natural selection Penicillin  Penicillin is derived from Penicillum mould. It was the first antibiotic drug based on a naturally occurring substance. After 4 years of use, 14% Staphylococcus strains were resistant to the drug. By 1950, over 50% of strains were resistant. o Zone of inhibited growth: on a petri dish, penicillum mold emits a chemical that kills nearby Staphylococcus o Antibiotic resistance is an example of microevolution by natural selection  Population: individuals of a species in the same place at the same time  Phenotypic Variation: heritable variation in appearance and/or function; phenotypic plasticity  Quantitative Variation: characteristics with a range of variation controlled by multiple genes; measured data  Qualitative Variation: characteristics with distinct states that can be observed behaviorally (ex: Mendel’s peas, garden snails varying shell colours) o Polymorphisms: distinct variants of character (ex: colour of peas can be yellow, green)  Trait’s variation is different across populations of the same species (ex: human height is distributed differently across countries)  Quantitative can be graphed in a distribution, qualitative traits must be grouped Genetics vs Environment  Phenotypic variation is due to a mix of genetics and environmental factors. Experiments can be conducted to determine the connection between genotype vs. phenotype. Keeping genetics constant to determine environmental factors to exclude them from genotype. o Breeding experiments, selection experiments o Hydrangeas change colour depending on pH of the soil, non genetic  Experiment on the physical activity of mice: o 4 control (random breeding), 4 experimental (only breed most active). After 10 generations of breeding, experimental mice increased in activity and variation was reduced compared to control. Genes not contributing to activity level trait were removed.  Mutation causes genetic variation o Recombination/crossing over, independent assortment, random fertilization o Can artificially select traits to breed (dogs, Brassica)  Can measure genetic variation directly using DNA sequencing methods such as PCR HARDY-WEINBERG AND AGENTS OF MICROEVOLUTION- LEC 26  Gene pool: sum of all alleles at all gene loci in all individuals o can calculate genotypic frequencies and allele frequencies o P= allele 1 frequency, Q= allele 2 frequency; in a diploid allele pair W/R W/R  Genotypic frequency represents how C C alleles are distributed among individuals (45%, 50%, 5%)  Allele frequency represents the commonness of each allele in the gene pool (0.7, 0.3) o P + Q = 1  Hardy-Weinberg Equilibrium: frequencies of alleles and genotypes in a population will remain constant through generations provided only Mendelian segregation and recombination are at work. Shows what you would expect to find in the next generation. o P +2PQ+Q 2 o Null model of evolution, compare this to real population o Possible when conditions are met: 1. No Mutations 2. No gene flow 3. Population infinite in size 4. No natural selection 5. Individuals mate randomly Agents of Change 1. Mutation: spontaneous, heritable variation in DNA  Rare event, significant over long time scales  Major source of heritable variation, effects all other agents  Deleterious: mutations that are harmful to organism, can persist if recessive  Neutral: silent mutation that does not change amino acid, amino acid that does not change the protein  Advantageous: benefits organism, favored by natural selection 2. Gene Flow: migration, movement of alleles across different populations  Migration of individuals (seed) or gametes (pollen)  Life history, behavior may enhance  Dispersal agents (blue jays, burs carried on animals, cargo boats picking up marine water and dropping it into freshwater environment) 3. Genetic Drift: random change in allele frequencies  Smaller populations reduce genetic variability  Population Bottleneck: drastic reduction in population size by a catastrophic factor, reduces alleles  Founder Effect: few individuals starting a new population from a larger population  Can lead to fixation of alleles (Kakapo) 4. Natural Selection: individuals with certain traits tend to survive and reproduce at higher rates  Includes sexual selection  Nonrandom survival  Relative Fitness: contribution an individual makes to the gene pool of the next generation, ability to survive to reproductive age and have fertile offspring SELECTION AND MAINTAINING VARIATION- LEC 27  Directional Selection: favors individuals near one end of a phenotypic spectrum o Small beaks favored  Stabilizing Selection: favors individuals with intermediate phenotypes o Goldenrod gall fly vs. Eukrytoma Gigantea parasitic wasp both lay eggs within Goldenrod gall. Wasp eats fly larvae and mostly feeds on small galls. Picoides Pubscens Woodpecker predatory bird favors feeding on larger galls. Therefore, flies in intermediate galls have highest fitness.  Disruptive Selection: favors extreme phenotypes o Small or large beaks favored  Sexual selection: competition for mates o Can be between rivals (fighting), or for affection of mate (performing) o Grey Tree Frog experiment: took eggs from female, fertilized with both short and long call frogs. Long call frogs were larger in size after 2 years, explains why females favor them. Short call frogs had some success, selection was not absolute Natural selection can balance polymorphisms  Heterozygote advantage o Sickle cell: Homozygous for sickle cell allele die before reproductive age. Heterozygotes are resistant to malaria. Selective force for HA HbSgenotype in regions where malaria is high  Frequency-dependent selection o Fitness of a genotype increases as its frequency decreases, rarity is favored o Predators go after most abundant prey o Rover vs Sitter: 3 conditions- more rovers, more sitters, equal amount of both. Glow stained fruit fly larvae, food source (yeast) challenged, concluded that more rare larvae was most successful at feeding when yeast was low.  Adaptive traits: products of selection that increase relative fitness  Adaptation: accumulation of adaptive traits over time o Some traits arise by chance, not selection o Current structures derived from previous structures  Limitations on natural selections: historical constraints, chance, adaptations lag on environmental change DARWIN AND EVOLUTION- LEC 28  Natural history: biological study of organismal form and variety in natural environments  Taxonomy: biological classification of organisms, Linnean for “greater glory of God”  Biogeography: world’s distribution of organisms. Exploration raised question in “unchanged creation”  Vestigial structures: currently useless structures ex: Tailbone  Stratification: horizontal layers of sedimentary rocks held fossils between layers, suggest extinction of some species  Paleobiology: study of ancient organisms  Jean Baptists Lamarck: proposed incorrect theory about use/disuse but was correct about: o Species change with time and pass on those changes o Organisms respond to environment o Use and disuse: Giraffes necks stretched each generation to reach tree leaves (useful)  Robert Grand and Henslow were friends of Darwin’s. Henslow suggested to Captain Fitzroy to bring Darwin as a naturalist along on 5 year voyage to South America. On this voyage Darwin noticed: o Giant fossilized sloth and armadillo o Seashells on mountain o Morphology of tortoise shells varied with location o Marine iguanas  Malthus “Essay on Principle of Population”: explained that as population grew, food supply would be limited. Should not support poor or unable. Inspired the theory of natural selection, challenged existing world beliefs.  Darwin co-published with Alfred Wallace some elements about evolution, later published his own famous Origin of Species. o Descent with Modification: fossils similarity share features with modern species, principle of succession o Divergence in Isolation from a Common Ancestor: fauna of Galapagos similar but distinct, different shell patterns on tortoises EVIDENCE FOR EVOLUTION 1- LEC 29  Laws describe, Theories explain  Evolution: Things gradually evolve and populations change over time. Speciation occurs when one species diverges into 2. All species share a common ancestor. Much evolution is caused by natural selection forces o Should see evidence of morphology, fossil record and DNA Sequencing o If common ancestor, should see transitional forms, retrodictions and vestigial characters Finches  Variation in beak size changes with different type of seed eaten  Peter and Rosemary Grant dedicated life to studying finches  Peter Boag study on Daphne Major: o Medium (Fortis) and large (Magnirostris) ground finches o Both prefer certain seed, spent 50% time eating it. After drought occurred and ruined seeds, spend 0.03%. o Magnirostris could eat spikey hard seed of Tribulus, got 1.5x more energy than Fortis would o Fortis took to eating Chamaescy, sticky seed that attached to feathers and pulled them out causing birds to die in heat o Decrease in population and seed abundance increase in hardness of seeds led to selection of Magnirostris. Fortis hatchlings were nearly 0.  Adaptation may be more evident in times of stress. Reduced variation occurs during bad years and wider distribution and variation fills in during good years.  Finches with deeper beaks show Bmp4 gene, also present in chickens. Expression of Bmp4 gene for the beak adaptation is significant. EVIDENCE FOR EVOLUTION 2- LEC 30  Karyotype of humans (23) vs chimps (24) chromosome pairs indicate a fusion event during speciation. Telomeric sequence on middle of chromosome in humans.  First detectable traces of life should be simpler forms  Fossil record: organismal features preserved long after death. Tissue imprinted in stone, lack of oxygen. o soft bodies less preserved o rare species may have not been fossilized o highly dependent on conditions  Otzi: 3300BC, oldest modern European found in Hungary, 5000 years old  Tollund Man: 375-200BC, Denmark, fossilized in bog (accumulation of dead plant material), acidic environment preserved skin and face.  Geological strata arranged in order formed oldest=deepest o Geological processes may move strata o Strata fossilized in represents relative age  Radiometric Dating: isotope half-life provides absolute age o C-14 emits electrons when burned, measure the number of electrons emitted to tell how much C-14. Use half life calculations to determine the original amount. Can now determine date of death  Cyanobacteria, 3.4 billion years ago, earliest life on Earth, provided oxygen to create more complex cell types o Fish 500 million years, humans 22 million years o 12:59:59 on a 12 hour clock of Earth’s existence  Marsh’s reconstruction of a horse shows small horse similar in size to dog growing and changing morphology. Food structure changed from toes with duclaw to hoof gradually.  Can take sediment from deep in the ocean and trace diatoms (protists) found long and short haline species  Transitional forms should be observed between species if from a common ancestor o Feathered dinosaur (sinornithosaurus) transitional form of birds and reptiles o Tiktaalik is transitional form between amphibians and fish  Retrodictions/Vestigial characters: o Whale came from hippo (water to land back to water) and water mammals formed. Water mammals develop hindlimbs in development but a genetic switch turns the expression of. Still sometimes if formed by mutation. o Bone structure at the end of a whale is similar to other land mammals spinal column with hindlegs  Vestigial genes: dead, non functional genes o Human fetal yolk sac, genes for making vitamin C  Retrodictions in biogeography: o Freshwater animals on oceanic islands o Mammals on continental islands are all similar to each other o Life on island similar to nearest mainland (Galapagos, Ecuador)  Convergent Evolution: similar niches occupied by different organisms (mammals and marsupials) o Evolution of the eye similar in octopus and human o Forces favor morphological features  Earth was one land mass (Pangea) that separated into different continents. Similar animals can be observed on each continent that evolved differently.  There are still imperfections in evolution: o Wisdom teeth remain after diet changed o Pharynx: breath and eat out of same tube o Hernias: occur in bipedal animals, groin stretched o Prostate: can cut off urinary tract CLASSIFICATION AND PHYLOGENY- LEC 31  6 Kingdom Classification: Bacteria, Archaea, Protista, Plantae, Fungi, Animalia  Phylogeny: evolutionary history of a species or group of species  Systematics: discipline focused on classifying organisms and determining their evolutionary relationships o Fossils, molecules, genes, DNA o Can help control pests, identify diseases, manage wildlife, choose animals for research  Latin scientific names used to avoid confusion with common names  Hierarchal Classification: Linneaus grouped into increasingly inclusive categories o Species – Genera – Family – Order – Class – Phyla – Kingdom – Domain o Represented using phylogenetic tree  Pleiotropy: multiple characters controlled by the same gene  Homologies: homologous characters result from common ancestry, similar structure and embryonic formation o Fundamental to systematics o Ex: Bones between human, cat, whale, bat all related  Homoplasies: analogous characters do not result from common ancestry, convergent evolution o Not used in systematics o Similar for reasons other than inheritance o Bird feathers are ancestral in birds, derived in all living vertebrates  Derived: a trait that differ from the ancestral trait o Can be determined from fossils and embryos, appear later in development  Ancestral: a trait that was present in the ancestor  Synapomorphies: derived traits shared among a group and are viewed as evidence of common ancestry o Ex: vertebral column of vertebrates  Evolutionary Reversal: a character reverts from derived back to ancestral trait  Monophyletic Taxa: includes one ancestral species and all its descendants  Polyphyletic Taxa: includes species from separate lineages, not intentionally used  Paraphyletic Taxa: contain an ancestor and some but not all descendants  Principle of Parsimony: simplest explanation likely to be correct o Minimize number of evolutionary changes must be assumed- fewest homoplasies  Traditional: uses phenotypic similarities and differences, based on distinct body plans  Cladistics: uses only evolutionary relationships o Groups all species that share derived traits o Clade: monophyletic linkage o Cladograms: tree made of clades Traits used in Constructing Phylogenies:  Morphology to describe species (skeletal system, floral structures) Some morphology is caused by the environment and some species show few morphological differences  Development: patterns may reveal evolutionary relationships (Sea squirts and vertebrates all have a notochord during development)  Paleontology: fossil provide data about past organism’s morphology, habitat etc. This is important in determining where lineages diverged to separate ancestor vs derived traits. The fossil record is incomplete so this is nearly impossible.  Behavior: can be inherited or culturally transmitted. Ex: bird songs are often learned  Molecular Data: DNA sequences now most widely used data for tree. Mitchondrial, chloroplast, nuclear DNA, amino acids all used. PHYLOGENY AND SPECIES- LEC 32  Phenetic Approach: based on computing a statistic that summarizes the overall similarity among populations. Software builds a tree that clusters similar populations  Cladistic Approach: focuses on shared derived characters of species (synapopmorphies- trait that only certain groups of organisms have) then placed in monophyletic group  Convergent Evolution: natural selection favors similar solutions to problems (dolphin/ichthyosaur), common cause of homoplasies  DNA sequences suggests close relationship between whales and hippos o Land mammals came from water, acquired astragalus (ankle bond) which is a synapopomorphy for artiodactyls (camel, cow, pig, hippo) Whales and hippos share 4 unique SINE (short interspersed nuclear elements) genes- 4,5,6,7  Outgroups are used to facilitate integration of time ex: turtle as outgroup for mammal phylogeny, share no traits  More taxa= huge number of possible trees  Molecular data are abundant, easier comparison of relationship, no environmental effect. RNA, DNA, amino acid change reflects evolution. BUT only 4 nucleotides, base changes may have evolved independently o Less similarity= distant on tree o Sequences must be aligned in the same position o Mutation can change DNA Length  Molecular Clock: rate of DNA mutation in different genome regions. Allows indexing time of divergence o Each DNA sequence has a different clock tick o Non-coding regions are more constant o Calibrate to fossil record PROTISTS- LEC 33- TREE OF LIFE  Evolved 1.2-2 billion years ago  Paraphyletic (some part of Plantae)  Structure: A membrane-bound nucleus, multiple linear chromosomes o Cytoplasmic organelles: ER, Golgi, mitochondria, chloroplast o Transcription and translation similar to eukaryotes o Unicellular, multicellular or colonies  Classification: o Collection of many kingdoms (paraphyletic) o Highly varied Eukaryotes o Not prokaryotes, fungus or plants o Not highly differentiated o Differ from plants: Photosynthetic, heterotrophic, no embryo protection (seed) o Differ from animals: no internal digestive tract, no complex development, no collagen  Habitat: aqueous; aquatic or moist locations such as oceans, freshwater, ponds, streams, moist soil, host organisms  Metabolism: aerobic, heterotrophic or photoautotrophic  Reproduction: sexual or asexual o Life cycles of cell division highly distinctive  Organelles: o Contractile vacuole: pumps water to prevent lysis in aquatic environments o Pellicle: layer of supportive protein fibres under plasma membrane o Pseudopodia: lobes of cytoplasm for amoeboid movement  Modes for locomotion include: amoeboid movement, swimming with flagella or cilia  Endosymbiosis theory: proposes that mitochondria originated when a bacterial cell took residence inside a eukaryote o Symbiosis: individuals of 2 different species live in physical contact o Endosymbiosis: one organism of one species lives inside another o Eukaryotic cells started to use cytoskeletal elements to engulf aerobic bacteria, lived symbiotically within host. Eukaryote supplied bacteria with protection and carbon compounds which it oxidized. Bacteria supplied host with ATP. Host cell was a predator capable of anaerobic respiration (fermentation) Bacteria yielded higher ATP so it was selectively favored.  Mitrochondria consistent with endosymbiosis theory because: o Size of bacteria is same as mitochondria o Replicated by fission o Double membrane from engulfing mechanism o Own genomes coding for enzymes needed to rep
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