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


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Date Created: 06/01/16
Bluegill sunfish smaller fish will sneak into territories to fertilize eggs whereas as larger fish will maintain territory so kind of an example for diversifying genetic and disruptive selection because middle intermediate phenotypes are selected against. Female Choice-males prove that they are healthy either by physical features, dances, how long to mate, which sperm gets to mate with egg (females can eject sperm from undesirable mate) Phenotype depends on the genotype and environment Variation at the phenotypical level is the sum of the variation in genotype and variation in environment Environmental variation: Leaves in sunnier location are more branched out whereas a leaf in the shade are less branched out Visible Genetic Variation: Polymorphism is discrete types; occurrence of two or more clearly different forms/alleles Quantitative Genetic Variation: genetics that deals with phenotypes that vary continuously Nonsynonymous Change: in beta-hemoglobin causes the sickle cell trait Nonsense mutation: a mutation in which a sense codon that corresponds to one of the twenty amino acids specified by the genetic code is changed to a chain-terminating codon. Synonymous mutations are like the Wobble Rule Nonencoding DNA can help regulate how genes are expressed. Exon: coding sequences. Transcription factors bind to the enhancer sequences or cis regulatory regions. Mutation in enhancer region can cause gene to be expressed less or more. **One species DOES NOT evolve solely for the benefit of another species **Natural selection may not work for the long term benefit of the species (not looking to see if they are doing the best thing for themselves and natural selection can lead to extinction)(Cannot tell how the environment will change over the time) **Natural selection operates at several levels and not just at individuals (at level of the genomic code as well) **Natural selection does not achieve the optimal phenotype for all traits (linkage when two genes are close enough on the chromosomes and have one gene selected for can bring along other genes on the chromosomes; not every trait will be at its highest level) Natural Selection: variation in a phenotype trait, heritable and survival Cancer cells and Natural Selection: The individual cells are the players in this selection; reproduction speed so some cells reproduce faster than others however too many cells will eventually kill the host and then natural selection may not work at the benefit Tasmanian Devil: transmissible facial cancer from playing Selection at the gene: Altruistic behavior so that you can pass on good genes to the next generation so that their genes get indirectly passed on (so take better care of the offspring); individuals work together to maximize offspring Kin Selection: natural selection in favor of behavior by individuals that may decrease their chance of survival but increases that of their kin (who share a proportion of their genes). Pleiotropy occurs when one gene influences two or more seemingly unrelated phenotypic traits. Consequently, a mutation in a pleiotropic gene may have an effect on some or all traits simultaneously. An example is phenylketonuria, a human disease that affects multiple systems but is caused by one gene defect. Irish Elk: natural selection for bigger antlers so they became more and more bigger in order to survive. However huge body mass was harder to survive. Speciation: the divergence of biological lineages and the emergence of reproductive isolation between lineages. Reproductive Isolation: a state in which two groups of organisms can no longer exchange genes (kind of happens by accident) Morphological Species Concept: look for individuals that look different from one another such as body size, features between different populations (field guide for birds) Biological Species Concept: groups of actual or potentially interbreeding natural populations that are reproductively isolated from other such groups; cannot reproduce then are separate species Speciation: the process by which one species diverges into two Geography -Allopatric: geographically isolated from each other and can diverge independently (can be caused by colonization when find mice genes on island were also on the coast); mtDNA inferred colonization Vicariance: Pockets of isolation; the geographical separation of a population, typically by a physical barrier such as a mountain range or river, resulting in a pair of closely related species. Secondary contact: contact between two species. Happened in Drosophila flies when there is a mixture of hybrid genes and two different species and weren’t completely reproductively isolated -Sympatric: divergence occurs even though the individuals in an incipient species are freely intermingling. Sympatric speciation is the process through which new species evolve from a single ancestral species while inhabiting the same geographic region. Speciation without specific isolation Polyploidy and hybridization is common in plants: -Parapatric: divergence of adjacent populations and speciation occurs: grasses that grew on mine waste versus grasses that grew on uncontaminated soil had natural selection to grow on these waste whereas uncontaminated grasses did not have to grow on the waste so hybrids of the two would be not suitable to live on either situations Examples of Colonization: -mitochondrial DNA, genetic DNA found in mitochondria of deer mice on California Islands and mainland Examples of Sympatric Isolation: -Cave fish living in crater lakes in Nicaragua Isolating Mechanisms: Premating Mechanisms: habitat segregation (use different resources), seasonal isolation (different breeding seasons such as Gyllus field crickets different times/months for eggs), behavioral isolation (such as specific flash patterns in fireflies in multiple species and they all have different mating rituals and visual, songs, smells/olfactory, tactile/connected with the sense of touch) Phermones: A pheromone is a secreted or excreted chemical factor that triggers a social response in members of the same species. A chemical substance produced and released into the environment by an animal, especially a mammal or an insect, affecting the behavior or physiology of others of its species. Pheromones are chemicals capable of acting outside the body of the secreting individual to impact the behavior of the receiving individual Tactile vibrations: spider tapping sounds creates vibrations on certain surfaces Post-mating, Pre-zygotic mechanisms: mechanical, gametic isolation, sperm competition, wind pollinated plants, post mating sexual selection Mechanical isolation: reproductive systems do not match, different insects store pollen on different parts of their body so plants will only and can only mate with their own species. Gametic isolation: different species have different proteins on the cell surface (sea urchin species have different receptors for the egg cell for specific sperm from their species; glycoprotein on the egg must match the receptor on the sperm), also Wind Pollinated plants Sperm Competition: c ompetitive process between spermatozoa of two or more different males to fertilize the same egg during sexual reproduction. Competition can occur when females have multiple potential mating partners. Greater choice and variety of mates increases a female's chance to produce more viable offspring. Post Mating Sexual Selection: when female mate to several mates/males before producing offspring Post-mating, Post-zygotic mechanisms: hybrid inviability or sterility (Goat and sheep mate but embryos die before formation) **How can a trait evolve that cause reproductive isolation? Dobzhansky Muller Model of Speciation: Needs to have mutations at two independent loci in order for hybrid to compatible when the two species come together. In the ancestral population, the genotype is AA BB. When the population is split into two, A evolves into a in one population and B evolves into b in the other. a and b are mutually incompatible. As the a-b interaction is not present in the pure species, the evolution of incompatibility is possible. In their model, a new allele arises and becomes fixed at one point. In the other now diverged lineage, a different allele arises at a different point on the gene. The two diverged species are now incompatible with each other because they have two alleles that have never been together in the same population. This changes the proteins that are produced during transcription and translation, which could make the hybrid offspring inviable or with very low fitness. Premating is a barrier beforehand; post mating barrier does form a zygote but it is not fertile and cannot Hybrid is fertile but cannot reproduce with the two species Premating barriers such as in Reinforcement would occur faster in the evolutionary sense in sympatric species Example: Nuclear Pore Complex Nup 160 and Nup 96 have different alleles but when together, form incompatible hybrids Rate of evolution of reproductive isolation: 0 is like mating two individuals from the same species and 1 is no offspring; genetic distance that gets larger shows more and more reproductive isolation Genetic Distance is a measure of genetic divergence between species or populations within a species Behavioral isolation: prezygotic isolation seems to have more isolation than post zygotic Reinforcement: is when Behavioral (prezygotic) isolation evolves more rapidly in sympatric populations; increased behavioral isolation between sympatric species You may get some mating but they become less fit so gives rise to stronger prezygotic isolation. Phylogenetic: a system of classification of organisms based on their developmental  relationships rather than their overall similarity of form Molecular Clock: the average rate at which a species' genome accumulates mutations, used to measure their evolutionary divergence and in other calculations. Average rate at which a given gene or protein accumulates changes to gauge the time of divergence for a particular split in the phylogeny. Genetic Distance: is kind of like the time The longer it has been, the more mutation arises **The chance of a mutation going to fixation is: 1/(2N) **2Nu per base pair is the rate of input of “new” alleles/mutations in a diploid species Replacement is just the number of mutations that go to fixation Time it takes for a mutation to go from substitution to fixation is 1/u because the first thing you need to do is recognize that u is mutation rate correct? So what is a rate? Rate is a change in something over time (in this case, the change in a gene over a certain number of generations). But the question wants us to find the inverse of that, it wants us to find the number of generations it will take for a change in a gene to occur. So if u is fixation rate/generations than 1/u must be the number of generations per a fixated gene. Hence 1/u will give us the number of generations before the fixation of the next variant. K (sequence divergence) = 2 t u (rate of molecular evolution); u stays the same and as K increases, the time also increases. -Time since speciation will correlate positively with sequence divergence; more time passed will have more sequence divergence Taxonomy: description, naming and classification Systematics: evolutionary history of adaptation and diversification (such as biogeography and ecology) of a group; how something has gone through adaptation and diversification in its history to evolve Phylogenetic: inference of evolutionary relationships of populations, species, or genes Phylogeny: inferred pattern of relationships, represented as a phylogenetic tree Evolutionary Forces cause change in allele frequency: nonrandom mating, migration, mutations, natural selection. Interestingly enough, in small populations, sampling errors can cause allele frequencies to change randomly from generation to generation. The effect of chance in small populations can lead to genetic drift--changes in gene frequency due to random events. The smaller the population, the greater the chance of having random deviations from the average. Such random events may lead to a change in allele frequencies within the population. The founder effect and a population bottleneck are two examples of random drift that can have profound effects in small populations. The founder effect occurs when an entire population descends from a small number of individuals. Such a situation produces a population whose gene pool is a tiny sample of the original and the frequency of any allele within this population is likely to be different from that of the original population. BIO Lab #1 Locus: the specific site of a gene on a chromosome; all alleles of a particular gene occupy the same locus Allele: one of the alternative versions of a gene at a given location or locus on a chromosome Population: Gene Pool: the total number of genes of every individual in an interbreeding population Genotype: genetic constitution makeup of an individual Phenotype: the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment. Genotype frequency: Genotype frequency in a population is the number of individuals with a given genotype divided by the total number of individuals in the population. Allele frequency: This is a measurement that determines how frequent the allele expression of a particular gene arises in a population; chromosomes that carry that allele. Phylogeny Terminology Moving downward we get older and older Ingroup: group that we are interested in Outgroup: outgroup lets us see what the common ancestor looked like; a species or group known to be closely related to but phylogenetically outside the group of interest Clade: includes common ancestor and all of its descendants and offspring Node: at the end is taxa that is presently alive Node: the point where each branch crosses Root: common ancestor of all the species that we are interested in/the base of the tree/branch we are interested in Branch: each vertical line Distance Scale: give us some sense of the amount of divergence; average rate of change of some sequence


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