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Perspectives of Biology 113 Notes

by: charlotteee

Perspectives of Biology 113 Notes

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Second semester of a two-course introductory sequence for students with a strong background and interest in science. Topics include: evolution, organismal diversity, ecology, and functional biology...
Perspectives in Biology 113
Class Notes
Bio113, Perspectives of Biology




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This 6 page Class Notes was uploaded by charlotteee on Wednesday June 1, 2016. The Class Notes belongs to at University of Rochester taught by Bickel in Spring 2016. Since its upload, it has received 7 views. For similar materials see Perspectives in Biology 113 in Biology at University of Rochester.


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Date Created: 06/01/16
Common/shared ancestor (shared mechanisms used in different contexts in different organisms) Tissue types=cell differentiation, diversity of species occupy their own niche, genetic variation between species but also between individuals. How common/central mechanisms play in the entire picture Multicellular individual will have cell differentiation Charles Darwin’s Ideas: Descent with Modification (descent with modification from a common ancestor); Natural Selection Soma cells: aren’t going to contribute to the next generation (altruistic, mortal) Germ cells: form into an organism for next generation (immortal) Selfish Genes: a gene that exploits the organism in which it occurs as a vehicle for its self-perpetuation; adaptive evolution occurs through the differential survival of competing genes, increasing the allele frequency of those alleles whose phenotypic trait effects successfully promote their own propagation Regulation in Gene expression: Enhancer sequences are regulatory DNA sequences that, when bound by specific proteins called transcription factors, enhance the transcription of an associated gene. Regulation of transcription is the most common form of gene control, and the activity of transcription factors allows genes to be specifically regulated during development and in different types of cells. Transcription factors can bind to enhancer sequences located upstream or downstream from an associated gene, resulting in stimulation or enhancement of transcription of the related gene. Correlation versus Causation: Positive correlation (A goes up, B is going up, A causing B to go up) (some other factor, X is causing A and B to go up) (B is causing A to go up) Correlation rates correlate even without any causation behind them Proximate Causes: genetic, biochemical and developmental basis for variation (Bmp4 causes beak size) Ultimate Causes: how did processes of mutation, natural, selection and evolution bring about differences (why do these birds need different beak sizes?) Tactics to do Science: -Observation (discover patterns in nature; where species are in the world, what the DNA sequence of a specie is) -Theory (make observations to explain these patterns) -Experiments (to test these ideas and theories) Mathematical Models: formalized hypothesizing, making assumptions clear and unambiguous, Functional mapping of outcomes (dependent variables) on conditions (independent variables) Manipulate control, have multiple samples, replication, controls, avoid pseudo replication and mix up the samples Evolution: a change in time; a change in allele frequency Secondary contact: when two species start to diverge in allopatric locations and then come back together in contact which leads to reduced intercrossing in areas of secondary contact Evolutionary theory: observing physical changes over evolutionary time, evidence on how these changes occur and about what evolutionary changes have occurred in the past. Evolution: changes in the genetic makeup of populations over time. Population: group of individuals of single species that live and interbreed at the same geographic area at the same time. Individuals do not evolve, populations do. Natural selection, gene flow, genetic drift and nonrandom mating all affect genetic makeup of populations over time. Gene Pool: sum of all copies of all alleles at all loci found in a population. Sum of all genetic variation in the population. Proportion of each allele in the gene pool is called the Allele Frequency. Proportion of each genotype among individuals in the population called genotype frequency. Adaption: a favored trait that evolves through natural selection. Natural selection removes deleterious mutations from populations Gene Flow: migration of individuals and movements of gametes between populations can change allele frequencies in a population. Genetic Drift: (smaller populations) random changes in allele frequencies from 1 generation to the next and may produce large changes in allele frequencies over time. Mutation: source of new variation in which natural selection and evolution can act on. Nonrandom mating can change genotype or allele frequencies A population with more than one allele at a locus is called a polymorphic . Leads to polymorphism. Hardy-Weinberg Equilibrium: Individuals with different genotypes have equal probabilities of survival and equal rates of reproduction. No gene flow -Deviations from the Hardy-Weinberg equilibrium show that evolution is occurring. Traits that show continuous quantitative variation rather than discrete qualitative variation are called quantitative traits. Stabilizing, directional and disruptive selection Divergent species share a common ancestor, species are not immutable; they change over time Silent substitution/Synonymous substitution: nucleotide substitution that does not change the encoded amino acid. Do not affect functioning of a protein. Missense substitution/Nonsynonymous substitution: substitution that does change the amino acid sequence encoded by a gene. -Substitution rates are highest at nucleotide positions that do not change the amino acid being expressed. Rates are even higher in pseudogenes (copies of genes that are no longer functional) Neutral Theory: most gene variants confer neither an advantage nor a disadvantage so neutral variants accumulate through genetic drift rather than positive selection -Heterozygous individual more likely to outperform individuals that are homozygous for either one of the alleles because two different alleles can survive and perform under more different situations. Evidence of Evolution in Seven Steps: 1. Fossil Records (extinct species and groups), transition fossils, morphology looks similar to other species; organisms change over time, abundance of species change as well; Times when there are a lot of species and fewer species (speciation events), Humans also changed over time. Looking at Stratigraphy: the branch of  geology concerned with the order and relative position of strata and their relationship to the geological  time scalto tell how old these fossils are by the deposition of soil on top (newer species on top and older on the bottom). Sometimes doesn’t layer up the way we expect (The Great Unconformity) due to geological rock movement 2. Homology of Parts: functional parts: incredible similarity in how they are built (ex: have the same number of bones, common structure) = common ancestor Homology of Genes: Hox genes (patterning, end and front tissues of species, help lay out the basic body forms of many animals); same genes are related to one another and doing the same function. Imperfect Design: penguins and wings. Vestigial Organs: hind limbs in snake and sperm whale: parts leftover from ancestor and organism has to build upon what was there. Gene in the eye of a fly will make an eye in a mouse; closely related creatures share more DNA 3. Embryology: common looking-common developing mechanisms; evidence from mice can provide many clues what can happen to humans because of similarity/homology of genes 4. Hierarchical Classification of Organisms: Relationships between organisms by the way of classifying them. Linnaeus: Order -> Family -> Genus -> Species, more recently split=more similar species; shows common ancestor. Species can be classified to see if they have a common ancestor in the past 5. Biogeography: closest relatives on mainland, related species on isolated islands. Marsupials all/mostly in Australia, Darwin’s finches on Galapagos Islands. Relationships between different organisms and where they are located. Movement of tectonic plates so marsupials that couldn’t have swam across got to other lands Gondwanan Distribution Continent: common ancestor that lived of supercontinents called Laurasia; typically when the organisms are restricted to two or more of the now-discontinuous regions that were once part of Gondwanan. 6. Artificial Selection: selectively breeding to change how organisms look; selection by humans of animals and plants with desirable characteristics for use in breeding over several generations. Farmers and breeders allowed only the plants and animals with desirable characteristics to reproduce, causing the evolution of farm stock. This process is called artificial selection because people (instead of nature) select which organisms get to reproduce The more insulin-like growth factor, the smaller the body size (weight) of the dog 7. Rapid Evolution in Nature: unintended causes and effects of human activity cause evolution; houseflies changing through time to adapt to these insecticides on Danish farms. Peppered moths evolved to become from lighter to darker colors during the Industrial Revolution (to prevent predation from birds if they were white and the ash on tree barks were darker); If evolution were true, you would expect unrelated species to have evolved to come up with similar solutions. Mice have different color fur depending on the environment Mc1r variant: causes red hair and fair skin in humans Agouti gene: makes fur color of mice very darker Mechanism of evolution is Natural selection! Natural selection: variation among individuals in some phenotypic trait such as morphology, physiology, behavior. Variation is heritable, and offspring look like parents, non-random differences in survival and fertility/reproduction due to that variation. Individual variation needs to be inheritable and can be passed down in generations Three conditions must be met for selection to occur in a population: 1. Variation: Individuals in the population must differ with respect to the trait in question. Without this variation, all individuals will have the same trait value and cannot be distinguished with respect to that trait. 2. Heritability: The variation found in the population must (at least partially) be heritable, e.g. transmitted from parent to offspring. If the variation in the trait was due entirely to the environment, for example, changes in the parent population would not affect the characteristics of the offspring population. 3. Differential Mortality: Finally, individuals must have a probability of survival that is a function of the value of the trait in question. If all individuals, regardless of their trait value, had an equal probability of survival and fecundity, no predictable change in the mean value of the population would occur. Consequences of Natural Selection: Differential representation in next generation (increased frequency of alleles that confer higher fitness) = Evolution (so the phenotypic trait needs to have some advantage) Divergence of different populations = origin of new species Daphne Major Island (Grant & Grant): evolution of birds, individual birds evolving and becoming bigger because the seed cases are becoming harder and bigger due to drought and the birds need to be bigger in order to crack open the seeds Beak Size in G. fortis: large brown finches were better at cracking seeds so medium sized finches evolved to have smaller beak size to specialize so they did not have competition Regulatory DNA: how often a gene is turned on or turned off. RNA polymerase can be recruited in different tissues. DNA in the upstream such as promotors, operators, and enhancer sequences help recruit or inhibit RNA polymerase binding to the gene and transcribing the gene Types of Selection (at the phenotypical level): Stabilizing Selection- if individuals close to the mean have the highest fitness, the mean does not change but variation is reduced on the edges, individuals at the extremes are selected against; higher frequency of that trait Directional Selection- if individuals at one extreme have the highest fitness, there is an evolutionary trend toward that extreme. Ex: threespine sticklebacks individuals with smaller number of plates were more likely to survive and reproduce; extreme trait favorable Disruptive Selection Within a Species (Different from two populations looking different from each other)- if individuals at both extremes have high fitness, variation in the population is increased, and a bimodal pattern may result (not as common in nature). Ex: black bellied seed crackers: smaller birds better at cracking softer seeds, and large birds hare better at cracking large seeds whereas middle sized birds do not thrive as well. We don’t see this is as often because a low and a high individual will always mate with each other and will bring us back to the mean. Environmental pollution can drive disruptive selection to choose different colorings in animals for survival. Selection at the Level of Genetic Variants: (Inbreeding can result in deficiency of heterozygotes) Negative/Purifying Selection: removing deleterious mutations, selection against new mutations, variants, to purify the genome; if there is a new gene and that new gene is deleterious, then selection is going to move towards getting rid of that gene Positive Selection: selection for an allele the increases fitness such as a mutation that makes resistance of insecticide (from a G to A mutation), one allele having a higher frequency, change to make organism more fit Diversifying Selection within a species/population: selection to increase the number of alleles; almost like disruptive selection (like immune genes, mating genes in plants); natural selection selecting for two or more distinct phenotypes that each have their own advantages and intermediate phenotypes are less fit Genetic Variation: environment and genetics lead to phenotypical variation Genotype-Phenotype Map: changes in genotype but not as much change in the phenotype because some genotypes may be synonymous so not a one to one ratio; incredible amount of DNA but didn’t tell us everything Sexual Selection is just a type of Natural selection: not all selection leads to an increase in fitness to external environment (usually not due to the external environment but with other individuals in the species). Selection is to increase chance of survival and reproduction and not just fitness to the external environment, just make sure genes get passed on to the next generation; organism’s ability to obtain a mate Anisogamy: reproduction by the fusion of dissimilar gametes differing in size and or form; fertilization between mates of unequal size, unequal gamete sizes. Males produce more sperm than females producing eggs and males potentially can mate with more females than vice versa. Females chose males that can maximize offspring fitness because much more investment. Types of sexual selection: Male to male competition-males compete for access to females, number of males have physical features or maintain territories and have better access can get more females, more healthy = better genes Sexual dimorphism: males much larger than females, and genders exhibit different features other than reproductive features. Reasons for sexual dimorphism: good genes hypothesis (having huge display is indicator to female that you have good genes; indicator of how good your genes are) Runaway Sexual selection (females select for males for certain traits such as bright feathers and then the males become even brighter in which causes the females to like this trait even more)


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