FINAL Study Guide

Chapter 7: Neutral Theory

• Know the theory and the experiments that support the theory
  • Use of pseudogenes to establish a canonical rate
  • Molecular evolution in the influenza virus
  • The role of functional constraints
  • Neutral mutations do not vary among species: The effects of population size and generation time

Using Neutral Theory as the null hypothesis

• Using the ratio of nonsynonymous mutations to synonymous mutations to detect selection
• The M-K test--selection occurs at particular loci
• Codon bias
  • Fig 7.24, codon bias seen in more highly expressed genes

Why is neutral theory important?

Chapter 19 Development and Evolution

• Define what is Evo-devo
• The role of homeotic genes in determining body plans and animal diversification

  • Deep homology
  • Study of onchyphorans

  Examine how chemical signals control development of multicellular animals
  • How are arthropod segments specified?

    • Wingless, engrailed, distalless  genes
  • How does a limb develop?
    • Molecules involved in setting up the 3-D axes
    • The role  unique patterns of expression
• Characteristics of the ancestral bilaterally symmetrical animals

Chapter 20: Human Evolution

• Molecular and morphological evidence of human relationship to chimpanzees and gorillas
  • Know the phylogeny
• Fossil evidence
  • Referential modeling and adaptive suites
  • Know the adaptive suite set forth by Lovejoy for Ardi. Lovejoy article is on Georgia View

Understand what is a molecular clock and be able to calculate  the age of the common ancestor of an HIV virus given slope and y0 (HIV Clock).

By special request: Producing a phylogentic tree on the domestication of the dog. OR a Hardy-Weinberg Problem (Extra credit)

The other chapters

Chapter 1

• Know the life cycle of AIDS
• why are some people resistant to AIDS?
• What was the origin of AIDS?
• How does AIDS evolve in an individual?
• Follow discussion of AIDS in other chapters, in particular the CCR5 D32 allele

Chapter 4

• Understand and be able to use the term synapomorphy
• Use of parsimony in distinguishing homology from homoplasy
• What are homoplasius traits?
• Know the whale case study and how it is used to show the importance of using different data to assemble a phylogenetic tree
  • What were the two hypotheses?
  • What morphological and molecular traits were examined and which trees did they support?
  • What methods are used to evaluate a tree?
  • What method is used to evaluate a tree branch?
    • Know how bootstrapping is used
  • SINEs and LINEs
  • Additional fossil data
• Know what the terms systematics, monophyletic and paraphyletic, polytomy refer to

Chapter 10

• The different ways of studying adaptation
  • Experimental evidence, Know the important points of experimental design and the importance of replications
    • The function of wing markings and wing waving display of the Tephritid fly.   Know the hypotheses and predictions.
  • Observational studies, when are they appropriate? what makes a good observational study
    • Adaptive choices used by garter snakes.  How did this study illustrate a good observational study?
  • Comparative method, how to test correlations--The Felsenstein Method
    • Bat testes and sperm competition

Chapter 16

• Mechanisms of genetic isolation
  • The 3 stage process
  • Allopatric speciation
    • Dispersal and colonization Drosophila  study
    • Vicariance Snapping shrimp study
  • Role of mutation: polyploidy and plants and other chromosome changes
• Mechanisms of divergence
  • Genetic drift and bottlenecking
  • Natural selection
    • The Hawthorne and apple maggot fly study
  • Sexual selection
    • Fighting Drosophila
• The role of secondary contact in speciation
  • Reinforcement through prezygotic and postzygotic isolation
    • Allopatric and sympatric speciation in Drosophila
  • Hybridization--the Helianthus study
  • Hybrid zones Table 16.3
  • Stabilization--the Sagebrush study