STUDY GUIDE FOR EXAM 1, BIOCORE(BCOR) 12 SECTION A, SPRING 2011

FINAL VERSION

Dave Barrington

The idea of this study guide is to focus your attention on the material you need to learn for the exam. The study guide does not mention all of the information covered in lecture, nor will the exam necessarily include questions from all of the topic areas listed in the study guide (it probably will). Remember that the exam covers the material from lecture: assigned reading that is not also in lecture material will not be on the exam.

MECHANISMS OF EVOLUTION

I. A Darwinian view of Life (Chapter 22)
    Alternative views from alternative data sets: bishop Ussher and the fossil record
    [Note: there is a slide on LaMarck in the powerpoint, but we did not cover LaMarck...unfortunately.]
    The structure of the fossil record: lower parts of a community below, older rocks below
    William Smith's map reveals the exposure of various ages across the south of England
    Cuvier and Brongniart: deeper rocks hold more exotic fossils; they infer evolutinoary change.
    Darwin's story: Henslow, Fitzroy, the Beagle, the Galapagos
       The finches: the data and Darwin's inferences; modern insights into the finches
       Back in England: the key influences on the development of the origin (Henslow, Malthus)
       The competition: Wallace, joint reading to the society, publication of the Origin of Species
    The five premises underlying Darwin's theory
    The evidence for descent with modification:
       homology [here just the pattern of shared features in equivalent positions, much better addressed in topic IV.]
       variation of domesticated animals and plants
       the vast amount of geologic time
       natural selection evident in the human population
    Observations explained by Darwin's theory:
       good fit of organisms to environment
       the shared characteristic of life
       the diversity of life

II.The Evolution of Populations (Chapter 23)
    Mendel's insights into genetics provided a mechanism for storage and release of variation.
    The new synthesis combined natural selection with the chromosomal theory of inheritance.
    Populations undergo evolutionary change; individuals undergo natural selection.
    Mutation and recombination yield the variation in populations that is subject to natural selection.
    Definitions relating to population genetics: population and gene pool
    Hardy-Weinberg equilibrium: a model for inheritance in the absence of evolutionary change.
          Make sure you can calculate genotype frequencies from allele frequencies and vice versa
    Assumptions of Hardy Weinberg equilibrium.
    Evolution as differential survival of different alleles in a population
        The hierarchical relationship of individual, population, and species in modern evolutionary biology.
        Kinds of Natural Selection
        Example of directional selection: the peppered moths
        Example of disruptive selection: the sky pilots [extra reading available, Galen]
    Genetic Drift and Evolution
        the bottlenexk effect - cheetah example
        the founder effect - Martha's Vineyard deafness example

III. The Origin of Species (Chapter 24)
   Biological species concept
   Kinds of reproductive isolation
   Limitations to the biological species concept
   Alternative species concepts
   The earth's immense diversity, its origin in divergence of lineages
   Anagenesis and Cladogenesis
   Allopatric and sympatric speciation modes
   Examples of speciation: antelope squirrels and mimulus flowers [extra reading available, MacNair]
   Polyploidy, a clear case of sympatric speciation
   Sympatric speciation through sexual selection in cichlid fish
   Hybrid zones: divergent evolution as reversible
   Tempo: Darwin's gradual change versus Gould and Eldridge's Punctuated Equilibria
        Example of punctuated equilibria from recent research, columbine spurs [extra reading available, Whitten]

IV. Phylogeny and the Tree of Life (Chapter 26)
  The components of systemtics are speciation, taxonomy, and phylogeny.
  Brief review of taxonomy, including binomials, hierarchical categories, Linnaeus
  Phylogeny is the pattern of divergence history; phylogeny  is the basis of modern classification
  In modern phylogeny study, shared evolutionary innovations imply common ancestry.
  Evolutionary homology is the sharing of a derived character because of its inovation in
       a common ancestor.
  Serial homology is the underlying similarity of organs on different segments,
       discernible in spite of transformations for different functions.
At the molecular level, homology is based on position in the genome.
      Decisions about homology are made in spite of insertions and deletions in the DNA or amino acsid sequence.
      Homology can also be thought of as the sharing of stable regions of genes inherited from common ancestors.
      (Example: the homeobox gene and homoeodomain of its protein that determines how many arthropod segments have appendages.)
Parsimony: choosing the simplest explanation forwards the science fastest.
      Parsimony in phylogeny is choosing the tree with the fewest steps.
How to construct a cladogram:
      choice of outgroup
      polarizing character states (as ancestral and derived) -- a character shared by the outgroup and some of the study group members in ancestral
            [NOTE: ancestral and primitive mean the same thing.]
      inferring patterns of common ancestry
      building the tree by using shared derived characters to infer common ancestors
In phylogeny, a homology is the sharing of a character because of its innovation in a common ancestor, whether it's morphological or molecular.
Kinds of characters in cladistic analysis.    Apomorphy, synapomorphy, autapomorphy, symplesiomorphy.  
Kinds of groups in cladistic analysis: monophyletic, paraphyletic, and polyphyletic.

V. The History of Life on Earth (Chapter 25)       NEW NEWS --- NOT ON EXAM 1.