Study Guide Midterm 1
Study Guide Midterm 1 EEOB 3310 - 200
Popular in Evolution
Popular in Ecology
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Date Created: 09/18/15
Study Guide EEOB 3310 Evolution Test 1 Lecture 1 Biological Thought Before Darwin 82615 Greek philosophers were the rst reasoners meaning they did not attribute biological phenomena to the supernatural The believed life had no goal but could all be attributed to chance many accepting the idea of spontaneous generation Democritus developed the atom theory and believed there is order and increasing complexity in everything Greeks believed Earth to be eternal no beginning or end apocalypse Aristotle believed in eternal species everything is fixed and unchanging Renaissance brought about natural philosophers the closest thing to a scientist at the time Cuvier anatomist 1 Species were unchanging 2 Perfectly integrated anatomist is proof for divine creation 3 Variations are abnormalities copy errors 4 Evolution could not occur because everything already fit so well together 5 Extinction was real result of ooding like in Bible catastrophic theory Thomas Chalmers argued gap between Genesis 1 and 2 Hugh Miller days of Genesis each consisted of an epoch Buckland and Mantell discover dinosaurs in 1930 s Sedgewick discovered preCambrian fossils Paleontologists now know that fish precede reptiles which precede mammals in fossil record Richard Owen British anatomist 1 Coined term dinosaur 2 Acknowledged similarities between vertebrates as homologies very different mammals have same bones in roughly the same orientation 3 Believed in evolution did not agree with Darwin on mechanism Lamarck 1802 theory of evolution before Darwin parents pass traits which have been acquired down to their offspring Transmutation hypothesis Darwin s grandfather Erasmus claimed every animal had a common ancestor but he was written off as being old and crazy Robert Grant 1841 species change over time Robert Chambers 1844 fossils record evolution of species Wells pamphlet about human health concerning why certain people are resistant to certain diseases Didn t put together mechanism but hinted strongly towards an idea similar to natural selection Matthew botanist who explained natural selection in a book about trees Evolution was very political in the 1800 s and was associated with radical ideas change Owens why would God make three different ying vertebrates if there was a perfect way Geology Evolution change over time uniformitarianism replaces catastrophism Lecture 2 Charles Darwin the Voyage of the Beagle and the writing of On the Origin of Species 82815 0 Travel writing was big at the time of Darwin s voyage he became very famous simply writing letters and journals describing his findings 0 Darwin was supposed to marry his wealthy cousin Emma Wedgewood but instead he with the help of his uncle and grandfather convinces his father to let him go as a gentleman companion on this voyage 18311835 He is very excited to go but hates the ship life once he actually departs 0 Darwin was very wealthy he went to Cambridge and his favorite teacher was Sedgewick 0 Darwin read Lyell s book uniformitarianism on the HMS Beagle and the volcanic islands seemed to make more sense in the uniformitarianism theory than the catastrophism theory 0 Uniformitarianism is small changes building up catastrophism is large catastrophic events shaping Earth s biological and geological history 0 Darwin explored much of South America s inland noticed there was more biodiversity in the tropics yet still similar behavior in similar specimens 0 Arrived at the Galapagos Islands 4 years after leaving England These were volcanic much like the Cape de Verde islands off the coast of Africa but the fauna was not similar to that of Cape de Verde it was similar to that of South America which Darwin found very interesting This would mean that no God created animals specifically for their environments 0 Darwin knew that these volcanic islands were fairly recent geologically speaking but observed different but similar groups of organisms on each island 0 Island fauna almost always resembles fauna of the closest continent how do species adapt to a novel environment 0 Pigeon fancying was also very big at the time so once Darwin returned to England and published voyage of the Beagle he began to study pigeon breeding to try and figure out this mechanism for evolution 0 He knew that something was transferred between parents and offspring but knew absolutely nothing about genetics Began consulting farmers and breeders about how they select animals to breed what they are looking for etc 0 Reads Thomas Malthus essay on population Populations have the potential to increase very rapidly but there is a limit to resources Irish population 0 Darwin began to believe that nature was doing something analogous to what farmers do in artificial selection the difference is the selecting agent natural selection 0 Darwin loved barnacles 0 Alfred Russel Wallace comes along He was from a modest background and made his living as a collector Spent much time in the Amazon goes to the South Pacific Not formally educated but very smart Fauna on Flores vs fauna on Java He also comes up with the idea of evolution Almost dies of malaria also read Malthus essay and comes up with a very similar idea to that which Darwin has been working on for 15 years which was that nature favors organisms that are best suited to acquire resources Wallace sends Darwin a letter and Darwin is pretty upset with himself for waiting so long to publish He consults Lyell who urges him to shared Wallace s letter as well as some of his own work so this is what he does and Wallace s letter along with an essay is read to the Royal Society Darwin then publishes On the Origin he and Wallace become friends Lecture 3 Charles Darwin variation within species 83115 Took so long to publish Origin because he knew his beliefs were very radical and would take a lot of evidence to convince people and his wife Emma Wedgewood was very religious and he didn t want to upset her Darwin begins Origin with a discussion on the variation in plants and animals He spends a great deal of time defining species in the first few chapters talking about species vs variations Variation within species is very important because if a variation increases the ability to get resources then that variation will be more present varieties have the same general characters as species the amount of difference considered necessary to give to two forms the rank of species is quite indefinite Chapter 2 Audience is English gentry pigeons are very popular at the time Darwin wants to use the first couple of chapters to convince his readers that these are in fact processes that they see happening often in farming and pigeon breeder Wants a common agreement Talks about offspring having similar traits to parents also how artificial selection works and can enhance the desired traits This could also be a process acting in nature Fancy pigeons would not survive in the wild all pigeons descend from the rock pigeon Variation is naturally occurring and what occurs in nature is analogous to artificial selection Geography of variation is crucial In chapter 1 Darwin is attempting to get audience to agree with him by using pigeon and farmer examples He also acknowledges that he doesn t know as much as he would like to about the mechanisms of heredity PreDarwin explanation variation is a result of defective individuals Darwinian view intraspecific variation is present Aristolian view species and fixed and unchanging with an eternal essence Modern Synthesis view populations are well adapted to their environments Hubby and Lewontin work with allozymes data on genetic polymorphism collected by loading proteins onto a an agarose gel and passing an electric current through Different amino acids have different charges and will move through the gel at a different rate allowing geneticists to visualize allelic differences Mean heterozygosity is the average frequency of heterozygotes in a population across loci or the fraction of genes that are heterozygous in the genotype of average individual Percentage of polymorphic genes fraction of genes in a population with at least two alleles Lecture 4 Charles Darwin evolution via natural selection 902 15 0 Natural selection Darwin s argument for change over time A struggle for existence inevitably follows from the high rate at which all organic beings tend to increase Has to convince audience that nature is wasteful something people may not take kindly to 0 Immediate response to Darwin and Wallace s join paper was not very exciting people did not really care at first 0 Two goals of Origin 1 Convince his audience that species change through time 2 Provide a mechanism which explained this change 0 Darwin succeeds in his first goal but fails in his second This is a vehement argument until the Modern Synthesis Theory 1920s 1940s 0 Uses Malthus essay as an example for the fact that in every case there must be a struggle for existence 0 Malthus essay on population 1798 Population growth greatly exceeds number of resources therefore resources limit population size 0 In order to survive and reproduce an organism needs to be able to obtain resources respond to changes environment and avoid predators o Adaptation is an inherited trait that makes an organism more fit in its environment abiotic amp biotic which has arisen as a result of the direct action of natural selection 0 Hopi Hoekstra studies adaptation in mice Peromyscus polionotus Coastal populations have white sandy coats much like the beaches and inland populations are much darker Mice are hunted by visual predators so selection should favor a cryptic coat Mclr gene has to do with coat color in mammals Single SNP at one site where one nucleotide base is different Predation supplies selective pressure here biotic 0 Abiotic factors such as climate also play a crucial role in natural selection 0 Finches on Galapagos are good example of selective pressures acting on a population 0 Geospiza is genus and they arrived on islands about 23 mya molecular clock dating method 0 Peter amp Rosemary Grant have been researching finches on the islands since 1973 Daphne minor is very small and uninhabited by people allowing accurate census data 90 of finches die before reproducing o Finch population is variable found by collecting samples and measuring different traits o Is variation heritable Look for correlation between parent and offspring if trait is heritable locate genes that are the targets of selection 0 Is there variation in reproductive success 1 in 7 finches made it through the drought in 1977 Seed availability was low so competition was higher and seeds were harder o Is variation in survival and reproduction nonrandom Mean size of beaks before and after drought phenotype changed based on which finches survived o The long term nature of this study allows phenotypic traits to be tracked over dozens of generations Lecture 5 Gregor Mendel the Modern Synthesis and scientific publication 904 15 0 Natural Theology is a theological philosophy based on reason and empirical observation These naturalists felt that by observing nature they were becoming closer to God The world was viewed as perfectly organized and there was a desire to understand it Buckland described jaws of Megalosaurus as designed to provide food and minimize the pain to its victims To us this seems silly Publication of Origin causes people to think about separating science and religion Science should be practiced without theology Materialism all things that exist are matter Methodological naturalism observing Thomas Huxley says Origin is a machine gun in the armory of liberalism Known as Darwin s bull dog because he is a strong arguer who favors Darwin Second goal to provide a mechanism that explains change over time was a failure Darwin knew nothing about inheritance and believed it to be a blending of traits This was the major gap in Darwin s theory of evolution Theodore Elmer popularizes Lamarckism again Darwin did not believe natural selection could act fast which was also a problem Huxley and others believed saltation theories evolution proceeds in large jumps Modern Synthesis Hugo de Vries worked with the evening primrose and was the first to propose that hereditary material was located on chromosomes Was aware of Mendel s work and tried to take sole credit for it Found a 31 ratio in ower color Gregor Mendel was a monk who did many breeding experiments with garden peas Thomas Hunt Morgan replicated these breeding experiments using fruit ies because of their large chromosomes Drosophila Biometricians natural selection acts on traits that vary continuously Mutation theorists Medelians argued that Mendelian mutations were responsible for evolution J BS Haldane 10 papers showing that alleles with a slight advantage will come to dominate a population over time example used was peppered moth before and after industrial revolution Rate of mutation would have been much too high for this change in phenotype to be a result of only mutation so natural selection was accepted as driving force Haldane pioneered population genetics RA Fisher was first to describe phenotype as having an environmental and genetic component Showed a correlation between the magnitude of an alleles benefit in an environment and their rate of increasing Focused on human height Reservoir of genetic info allows for population adaptation A founder of statistics Fisher s fundamental theorem the rate in increase of average fitness of a population at any time that can be attributed to natural selection is equal to its amount of genetic variance at the time Populations with broad variety in fitness will adapt more quickly than those with little variation Sewell Wright very good at math coined adaptive landscape Like topography map there may be several regions of high fitness which natural selection works to build up or there may be one area which peaks above the others Different populations or a species may move toward different peaks Small populations inbreeding genetic drift process of change in allele frequency which results from chance rather than natural selection Theodosius Dobzhansky importance of genetic drift in small populations Ernst Mayr omithologist allopatry and sympatry defined species as breeding populations that were reproductively isolated from other populations GG Simpson paleontologist fossil record fits Modern Synthesis GL Stebbins botanist combined genetics and natural selection to explain plant speciation Natural selection does not explain all Genetics and sexual selection are very important Lecture 6 Genomes genetic variations and mutations 90915 Genomes contain the complete set of an organism s genetic material Typically this includes many chromosomes in Eukaryotes Number of genes dramatically differs across tree of life different species Great deal of DNA is noncoding Amphibians and owering plants generally have the largest genomes Vast majority in genome is noncoding 97 We don t know much about these noncoding areas Eukaryotes generally have larger genome than bacteria but there are many species of bacteria 2003 first draft of human genome Human genome project 197677 first sequences of RNA and DNA bacteriophages 2013 Homo neanderthalis sequenced Human Genome 23 chromosomes 20500 genes Share 50 of genes with bananas 93 of protein families have homologues in nonvertebrate organisms We can find homologies between us and very different species invertebrates decent with modification One of the smallest chromosome is human Y with 200 genes and 58 Mb Human genome could be compared to 2641 complete sets of Game of Thrones books Mutations Meiosis and crossing over 1 Duplication 2 copies 2 Deletion removal 3 Inversion segment is turned 180 degrees 4 Translocation segment moves from one chromosome to a nonhomologous chromosome Gene duplication extra copy may help the organism because if something goes wrong with one there is still another it may give more genetic material to work with also possible that new functions can be evolved by having more than one copy of the genes Copy A is carrying out its function so copy B has more room for evolution Genome duplication an important event in history of angiosperms Many adaptive radiations we know about are a result of gene or genome duplication Point mutations one base changing to another singlebase substitution in the sequence 1 DNA is constantly being unpackaged repackaged and there is room for error 2 We believe it occurs as DNA synthesis is taking place Usually DNA proof reading enzyme comes and xes it but it doesn t always 3 Transition a purine for a purine or a pyrimidine for a pyrimidine 4 Transversion a purine for a pyrimidine or a pyrimidine for a purine 0 Replacement nonsynonymous substitutions point mutations that change the sequence of the amino acid these can be selected in natural selection because the protein coded is actually different 0 Silent synonymous substitutions point mutations that do not change the sequence of the amino acid 0 C elegans has fast generation time Mitochondria lack some of the DNA proofreading enzymes found in the nuclear genome Chromosomal inversions Gene segment of DNA that codes for a distinctive type of RNA or protein product Many combinations codons can code for the same amino acids Stop protein Mutation s role in evolution 60 years where biologist debated the mechanism of evolution Mutation is not the primary reason Mutations are very small rate is usually XIOAS Mutation alone is not likely to be primary role in variation How many do we expect to see from one generation to the next Take genome size and multiply it by mutation rate for human genome we get roughly 80 this is such a small size that it s not likely to have an in uence most don t have any evolutionary impact Mu is in subssite generation 0 How do we estimate mutation rate in species with long generation times We can take a survey within a population or compare the genome in humans to those species which we are closely related Allows us to apply mathematical models and estimate mutation rates 0 Odds of mutation happening in two individuals independently is so low that if two individuals have the same mutation we ended up with it from an ancestor not from independent circumstances 0 Ne stands for effective population size The number of breeding individuals in an idealized population that would show the same amount of dispersion of allele frequencies variation under random genetic drift or the same amount of inbreeding as the population under consideration Sewell Wright 1931 0 Statistical concept that allows us to compare Strength of natural selection Equalizing different life aspects of different species 0 What genes in the human genome are still under natural selection Many are still under strong selection Purifying vs positive selection Many are associated with our brains many are also associated with olfaction Sense of smell is much less important 0 Almost any other species that has been looked at is under strong selection both positive and negative 0 Evolution Changes in allele frequencies within a population over time or the descent with modification in some lineage phylogeny 0 Observing evolutionary change requires a null model that predicts the probabilistic fate of alleles in the absence of evolution and a statistical test for determining when allele frequencies change to a degree that violates this null model Hardy Weinberg equilibrium Lecture 7 HWE and genetic drift 91115 0 Observing evolutionary change requires a nullmodel and a statistical test to determine whether a change in allele frequencies is significant 0 Punnett popularizes Punnett square as visual aid for predicting genotypes 0 Punnett is fan of Mendel s uses brachydactyly as an example for Mendelian traits in human populations Many other geneticists disagreed and argued that most traits don t follow Mendel s laws independent assortment and segregation Hardy takes Punnett square to a population scale with the HWE equation Laws of independent assortment can be extended to populations Weinburg published very similar findings which is why it is known as HardyWeinburg Equilibrium P2 2pq q2 1 Where p is equal to the dominant alleles in a population and q is equal to the recessive alleles If we have p then we have q because they equal 1 when added together P2 would be the percent of individuals in a population who had the homozygous dominant phenotype 2pq would be heterozygous and q2 would be homozygous recessive Assumptions of HWE 1 No selection alleles are not adaptive 2 No migration no introduction of new alleles 3 No mutation no new point mutations 4 No nonrandom mating every individual has an equal chance of reproducing with every other individual of the opposite sex 5 No genetic drift population size is large The equation is generally used as a null model and if what is observed is different than what is expected a chi test must be performed to verify whether the difference is statistically significant X2 observedexpected2expected There are degrees of freedom which must be used and if the X2 value is larger than the critical value obtained from the df then the change is significant If it is smaller the change is not significant HWE can be used to assess the deficit of heterozygotes in a population The mutation rates are so low that the probability of any two individuals having the same mutation is extremely low Therefore we conclude that any same mutation in two people was inherited by a common ancestor If an allele is present in all individuals in a population that allele is said to be xed The probability of fixation is much lower in a large population and is equal to the frequency of the allele in that population Fixation is bad because mutation takes some luck to make a huge difference Genetic drift is the process in which a loss of variation in alleles will lead to a change in allele frequencies over time Usually occurs in small populations Bad because it reduces genetic diversity Allele coalescence is when two alleles choose the same parent in the previous generation lN Lecture 8 Bottlenecks inbreeding depression gene ow and genetic drift 91415 Genetic drift removes variation in a population and acts with migration in the founder s effect to shift allele frequencies in newly founded populations Heterozygosity is the frequency of heterozygous individuals in a population The is lost at a rate proportional to the population size Hg Hg 1 12N Bottleneck effect over time a population will uctuate in size allowing genetic drift to act upon it Glacial periods climate change catastrophes etc Effective population sizes vary because of the differing number of offspring each individual produces there is overlap in generations there is not always a 11 sex ratio and there are uctuations in population size bottleneck Population subdivision Extreme forms of selffertilization will lead to a decrease in the number of heterozygotes in a population but not a decrease in either allele example snails 0 Inbreeding is very similar to this and can be incorporated into HWE by a coefficient F which is the probability that the two alleles in an individual are identical by descent p2l F pF 2pql F q2l F qF 0 Fst can be determined by solving 2pql F for F Fst is a measure of the difference in the probability that two alleles drawn from the population are identical to the probability that two alleles draw from the same species are identical As long as there is variation across species the populations will not be in HWE because the species as a whole will have a deficiency of heterozygotes This is the Wahlund Effect 0 Greater prairie chicken isolated small populations lead to a near extinction This was fixed by migrating other prairie chickens to the area to bring in new genetic variation gene ow This worked 0 Island Migration Model island and continental populations migration to island is significant migration to continent from island is not Pi 1 mPi mPc where m equals the proportion of migrants in one generation Api Pi 39 Pi 0139 Api mpc pi 0 Change in allele frequency due to migration is a function of both migration rate and the difference in allele frequencies from island to continent Absent of other factors migration would eventually even out all allele frequencies 0 Forces that decrease heterozygosity selffertilization nonrandom mating population genetic structure purifying selection directional selection genetic drift 0 Forces that increase heterozygosity mutation balancing selection outbreedingmigration and gene ow Lecture 9 Modeling natural selection 91615 0 Natural selection is inevitable if these are met 1 Variation 2 Inheritance 3 Differential reproductive success 0 Selection is always specific to an environment and acts on phenotype there is no goal 0 Fitness is a measure of the reproductive success relative to the average reproductive success in the population 0 Mean fitness is the product of the gamete frequencies and the survival rate Wbar P2 W11 qu W12 12 W22 0 Relative fitness is scaled by the fitness of the homozygous dominant group 0 S is the selection coefficient and is equal to the fitness of homozygous dominant relative to that of homozygous recessive H is the heterozygous effect and is a measure of the fitness of the heterozygote relative to the selective difference between the two homozygotes o Directional selection selection favoring one allele over the other 0 Balancing selection selection maintaining polymorphism Disruptive selection selection favoring the extremes of both ends Heterozygous effect equals lhs Anthony Clark Allison studied sickle cell anemia in Kenya He found that the disease though fatal persisted because heterozygotes would have sickle cells and normal cells meaning they were able to survive These sickle cells could not be infected by malaria so the disease persisted because heterozygotes were more fit than homozygous dominants Frequency dependent selection cost and benefits of an allele are generally proportional to their frequency in a population Lecture 10 Natural selection across loci Sexual reproduction has a cost only half the genes are passed to the offspring So why do it Rate of crossing over is inversely proportional to physical proximity In Linkage Equilibrium the alleles at each locus are independent of each other Genes on separate chromosomes are always in linkage equilibrium Some pairs which are close to each other are not independent These are genetically linked and at linkage disequilibrium Several evolutionary forces can create linkage disequilibrium but sexual reproduction eliminates linkage disequilibrium This is why so many organisms reproduce sexually Meiosis crossing over outbreeding Genetic recombination creation of new combinations of alleles during sexual reproduction Genetic hitchhiking neutral of slightly deleterious allele freq increases because it is physically close to an allele under positive selection Genetic draft term for this hitchhiking and it decreases heterozygosity in large populations Any locus can be in uenced by any nearby locus Epistasis the interaction among multiple genes that in uence a phenotype Recombination occurs during meiosis when chromosome arms cross over and exchange genetic material Extinction rates are higher in asexual organisms
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