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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
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Perspectives of Biology 113, Biology 113, Bio113
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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 8 views. For similar materials see Perspectives in Biology 113 in Biology at University of Rochester.


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Date Created: 06/01/16
Longer branches = longer time versus shorter branches = shorter time Monophyletic Group: common ancestor in all its descendants (like a clade); consists of an ancestral species and all its descendants Paraphyletic Group: (of a group of organisms) descended from a common evolutionary ancestor or ancestral group, but not including all the descendant groups. Dinosaurs are an example, some descendants are still alive today such as birds, reptiles Polyphyletic Group: Doesn’t include the common ancestor of the species; usually mistakenly grouped together; (of a group of organisms) derived from more  than one common evolutionary ancestor or ancestral group and therefore not suitable for  placing in the same taxon suchrouping birds with bats; does not include the common ancestor between the species Homologous: traits shared by two or more species inherited from a common ancestor Ancestral Trait: trait that originated in the common ancestor of the group we’re interested in Derived Trait: something that arose from that lineage (such as B from that state); a trait newly arisen since the divergence of two species from a common ancestor Homoplasy: a character shared by a set of species but not present in their common ancestor so the derived character is driven by convergent evolution and needed for the same needs Parsimony: simplest explanation that fits the evidence and lower the number of changes that happen; minimize the number of changes to build a tree Only shared derived traits are phylogenetically informative (B in this example); tells us that the two species will the B trait are probably more closely related together What is parsimony? The parsimony principle is basic to all science and tells us to choose the simplest scientific explanation that fits the evidence. In terms of tree- building, that means that, all other things being equal, the best hypothesis is the one that requires the fewest evolutionary changes. For example, we could compare these two hypotheses about vertebrate relationships using the parsimony principle: Hypothesis 1 requires six evolutionary changes and Hypothesis 2 requires seven evolutionary changes, with a bony skeleton evolving independently, twice. Although both fit the available data, the parsimony principle says that Hypothesis 1 is better — since it does not hypothesize unnecessarily complicated changes. This principle was implicit in the tree-building process we went through earlier with the vertebrate phylogeny. However, in most cases, the data are more complex than those used in our example and may point to several different phylogenetic hypotheses. In those cases, the parsimony principle can help us choose between them. Molecular Clock: a technique that uses mutation rate to deduce the time when two or more life forms diverged depends only neutral mutation rate Neutral Theory: most DNA is neutral means it is not under selection Mutation rate: fraction of gene copies in the next generation carrying the new mutation Mutation rate is represented by Chance of a mutation going to fixation: (1/2N) Time it takes for a mutation to go from substitution to fixation is 1/u Node: represent the common ancestor of some species Root: a basal node (the most recent common ancestor to all species of interest) Phylogenetically Uninformed characters: -Unique derived traits: Traits from outside influences or environments -Ancestral traits: traits that are in the common ancestor but don’t tell us how they affect the other newer taxa -Homoplasy: is characteristics of an organ that are shared by different species because of shared evolution but not present in common ancestor *A polytomy may mean that we don't have enough data to figure out how the lineages are related. There are six possible solutions to this polytomy. Often, gathering more data can resolve a polytomy. It is when more than two taxa whose relationship cannot be inferred. Conventional systematics: harder to infer which traits to value more than others Molecular phylogenetics: using DNA sequence; analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. Maximum likelihood: allows for variation in the probability of different changes; some changes may be more likely than others and therefore changes at the DNA level may not be equally likely to occur; proportional to the probability of observing the proposed set of data. Basically, this tree is our proposed data, so the likelihood that this is correct is the probability that it is correct. The goal is a tree that has maximum likelihood, or the best mathematical probability of being correct Transversion: Substitution in DNA and RNA of a pyrimidine for a purine, or vice versa, by mutation Bayesian analysis: efficient methods to explore parameter space and find the best tree to fit the data Distance Methods: using the total number of differences between taxa (not shared derived characters); find pair of species with greatest similarity (lowest genetic distance) and group together; instead of being based on shared derived characters, it’s based on the total number of differences between taxa **Evolution is changes in genetic material; Populations evolve by a change in their genetic composition Mendelian Genetics: when you have specific genotype frequencies produced with controlled crosses Populations Genetics: looking at whole population, frequencies produced in entire population, frequencies produced in entire population, incorporating mating system, natural selection, mutation, and random chance. Allele: distinct genetic variant. Can be defined in terms of measurable phenotypic effect or single nucleotide change Allele frequency: frequencies of different alleles. Basic unit of population genetics If Population is in equilibrium, its alleles and genotypic frequencies will stay the same P=frequency of dominant allele A Q=frequency of recessive allele (a) P^2 = frequency of homozygous AA Q^2 = frequency of homozygous aa 2pq = frequency of heterozygous Aa Hardy Weinberg Eq: in the absence of an evolutionary force a population’s allele and genotype frequencies remain the same. Assumptions of the Hardy Weinberg equation is that there is no mutation, non-random mating, no genetic drift, no natural selection no migration *dominant alleles spread faster through the population No genetic drift: population must be infinite size Probability of Survival: coefficient Number after selection divided by total number of individuals after selection Delta P= change in new minus the old Change in Delta q = negative delta p Delta P: how much P will change at a given allele frequency Protected polymorphisms: has a stable equilibrium and has protected polymorphism whereas unstable equilibrium. if each allele increases when rare, then there must be at least one stable equilibrium with both alleles maintained in the population Delta P: how natural selection is going to act on that allele Molecular Clock: For the past 40 years, evolutionary biologists have been investigating the possibility that some evolutionary changes occur in a clock-like fashion. Over the course of millions of years, mutations may build up in any given stretch of DNA at a reliable rate. For example, the gene that codes for the protein alpha-globin (a component of hemoglobin) experiences base changes at a rate of .56 changes per base pair per billion years*. If this rate is reliable, the gene could be used as a molecular clock. ******Mean fitness: the highest average fitness of the whole population **Natural selection will move the population mean fitness uphill Genetic Drift: is the random changes in allele frequencies due to sampling effects (we would typically see this in genes with little or no selective effects such as synonymous substitutions, pseudogenes Molecular Evolution: is the genetic change in genome, the RATE OF EVOLUTION DUE TO RANDOM GENETIC DRIFT (independent of population size and depends solely on neutral mutation rate) Genetic Drift: some point in history in which population got very small; random changes in allele frequencies due to sampling effects Impacts more when N is small; Small N (population) = large effect of genetic drift Increases sample size reduces random changes of allele frequency. Population size affects genetic drift, the bigger the population, the less allele frequency changes Genetic Drift types: Population bottleneck is when the population size is dramatically reduced and only a few individuals survive and their alleles are not representative of the entire original population (such as a drought altering allele frequencies). when a population is reduced dramatically in size over a short period of time due to some random environmental events Founder’s effect: new individuals end up in a new location with only a small amount of allele frequencies so they are not a real representative of entire population; FEW individuals colonizing new areas. Genetic drift as a result of a few individuals colonizing a new region Small population size is more likely to deviate from the parental group so big population is less likely to drift (Example: Tristan da Cunha: few men continue to live so example of genetic drift) By looking at DNA sequences, you can infer which genes have been under positive selection and see ancestral function of genes as well as how genome’s evolve P=0.5, if genetic drift acts on it, it will either go to fixation or become extinct (p=1 or p=0) P=0.7, means that there is a 70% chance to go to fixation and 30% chance that the allele with go to zero New mutations have small chance of going to fixation N=population size, Diploid = 2N, P=1/(2N) = probability to go to fixation


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