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Study Guide – Exam 1 – Bio508 9/22/04 This includes material through September 24, 2004. Material from the lecture on Sept 27 will not be on the test. I usually ask a couple of questions from student presentation, so please pay attention on Sept 22. 1) What are examples of homologous characters at the molecular and organismal levels? 2) What evidence supports the idea that organisms change over time? 3) What is the difference between absolute and relative dating of fossilized material? 4) Why, from evolutionary and developmental perspectives, are vertebrate embryos morphologically very similar? 5) Why are organisms often clustered geographically? 6) Compare artificial verses natural selection? What aspects of these processes are expected to differ? 7) You are given the wrong directions to a party and end up instead at a fundamentalist christian rally. You decide to engage a small group of people in conversation about evolution. How do you explain to them the following concepts or ideas: evolution by common descent, antiintellectualism, democracy and creationism, that hippos are the closest living relative of whales, that the earth is older than 5,000 years, that marsupials originated in North America and not Australia, intelligent design theory, and why creationism isn’t science. 8) With respect to the evolution of domesticated organisms (dogs, crops), what presumably provides the potential for such dramatic, and rapid evolution? Is this potential observed with different strains? In what ways do morphological patterns observed among dogs seem to violate Darwin’s model of evolution? 9) Although Lamarck is often chided, his theory of evolution was very different from Aristotle’s Scale of Nature. Compare their different ideas. 10) Compare evolution by natural selection versus evolution by genetic drift. What’s the difference? 11) Be familiar with the central tenets of the Modern Synthesis. 12) Why is recombination an important aspect of evolution? 13) How do specific mutational mechanisms (point mutation, inversion, unequal crossing over, gene conversion) affect the structure of DNA and the organization of genes? 14) What is the fate of duplicated genes? 15) Be familiar with the structure of DNA, including the specific classes of genes. 16) Why do some scientists think that regulatory gene evolution is more important than structural gene evolution? 17) Be able to apply the Hardy Weinberg Principle to calculate allele and genotypic frequencies (simple cases). 18) What is meant by the “strength of selection” in population genetics? 19) The example of HIV resistance in human populations highlighted two aspects of natural selection that influence allele frequency change. What were they? 20) Why does it take so long for an advantageous recessive allele to increase in frequency in a population after it originates? 21) Is possible for a lethal allele to be maintained at a relatively high frequency? Explain. 22) Although mutation alone is not a powerful evolutionary force, mutation is an important aspect of selectionist and neutralist theories. Explain. 23) Allele frequencies in populations may reflect a balance between opposing evolutionary forces. Please provide an example of this. 24) What is genetic drift and under what conditions do we expect genetic drift to be a relatively strong evolutionary force? 25) Does genetic drift result in adaptation? 26) Provide both the neutralist and selectionist explanation for the observation that two or more alleles are often observed for loci in natural populations. 27) Why are many alleles quickly lost in populations soon after they arise under the neutral theory? 28) In a relative sense, what are the fixation probabilities for neutral and advantageous alleles? 29) How does population size influence the rate of evolution (rate of allele fixation)/substitution? 30) What are the important results that derive from neutral theory? 31) Although population size doesn’t influence the rate of allele substitution it does influence the amount of genetic variation that is expected in a population. Explain. 32) Be familiar with the logic underlying the MacDonald Kreitman test. 33) What are the different types of natural selection and how are they defined in population genetic models? 34) What mechanisms influence the amount of genetic variation that is maintained in populations? 35) Is it possible for an allele’s frequency to be largely governed by genetic drift in one population, but by natural selection in another population? Explain. 36) What is functional constraint and why does functional constraint vary among genes? 37) What is meant by the rate of neutral allele substitution? 38) What type of gene is expected to show the highest rate of nucleotide substitution? 39) What gene regions are expected to show the highest nucleotide substitution rate? 40) Is the synonomous substitution rate expected to be higher or lower than the non-synonomous substitution rate for coding regions of a gene? 41) What pattern of nucleotide substitution is indicative of positive selection? 42) What is the evidence of positive selection at HLA loci, and why might selection act on these loci? 43) Why is the rate of substitution at 4-fold sites lower than the rate within pseudogenes? 44) What is codon bias and what types of genes are expected to show codon bias? Points to consider from Molecular Markers, Natural History, and Evolution From Chapter 2 (1) Compare and contrast the classical versus balance views of genetic variation in natural populations. (2) What molecular technique was first used to estimate genetic variability in populations and what was learned? Are there taxonomic patterns? (3) Why is it often observed that the level of genetic variation in natural populations of a species is lower than expected under neutral theory? (4) Why does Avise criticize allozyme multi-locus heterozygosity and fitness studies? (5) What is meant by selective sweep? (6) Review (not memorize) important events in the chronological history of molecular markers. From Chapter 3 (1) Read the entire chapter however focus most attention of the following techniques: protein electrophoresis, restriction analysis, animal mtDNA, plant organelle DNA, single copy nuclear DNA, PCR, microsatellites, AFLP’s, SINES, SSCP’s, and SNPs, and DNA sequencing. (2) What is meant by genetic distance and how is it estimated using DNA sequence data?