BIOLOGY 3301 Evolution Chapter 1

The virus and the whale: how scientists study evolution  
  1. Biological evolution
    • Biological evolution is the process by which inherited traits of a population change over time.
    • Any change in the inherited traits of a population that occurs from one generation to the next
  2. Evolution explains the diversity of life
  3. Understanding evolution has practical implications.
    1. How do pathogens become drug resistant?
    2. What is the source of new pathogens?
Outdoor photograph of an older man with thinning white hair, dressed in a suit.
Theodosius Dobzhansky January 24, 1900 - December 18, 1975
'Nothing in Biology Makes Sense Except in the Light of Evolution'
The American Biology Teacher, March 1973 (35:125-129)

1.1 Whales: Mammals Gone to Sea (p. 5)

  • Whales may look like fish, but closer inspection reveals they are more closely related to camels.

Terminology in section 1.1

  1. Lineage: a chain of ancestors and their descendants
  2. Character: recognizable attribute
  3. Convergent Evolution
    1. similar features from different ancestors in different lineagesas a result of ecological equivalence
    2.  convergence in placental and marsupial mammals- Dr. George Johnson's Backgrounder
  4. Homology: structural characters that are the result of shared common ancestry
  5. Synapomorphy
    1.  A derived trait shared by a group of related species that evolved in the immediate common ancestor and is shared by all of its descendants (although the trait may be modified or even lost)
  6. Phylogeny: a representation of the evolutionary history

Evolution case studies 1: Whales: mammals gone to sea

  1. How do we know whales are mammals?
    1. Whales share synapomorphies with mammals
      1. Mammary glands
      2. Three middle ear bones
      3. Hair (in developing embryos)
    2. Similarities with fish arose through convergent evolution
  2. Whale evolution (Fig. 1.8)
    • The molecular evidence indicates that hippopotamuses are more closely related to whales than they are to other artiodactyls. 
    • University of California Museum of Paleontology
    • Thewissen, J. G. M., E.M. Williams, L.J. Roe, and S.T. Hussain.  2001.  Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls, Nature 413: 277-281.  Philip D. Gingerich, et al.  2001.  Origin of whales from early artiodactyls: Hands and feet of Eocene Protocetidae from Pakistan, Science, 293: 2239-2242.
  3. Fossil whales share synapomorphies with modern cetaceans as well as more primitive characters (Fig. 1.4)
  4. Fossils reveal links to land mammals 
    1. Shape of astragalus connects to artiodactyls (Fig. 1.7)
  5. Fossil sequence documents transition from land to water
    1.  Pakicetus (Fig 1.5): a terrestrial whale
      1. involucrum
    2.  Ambulocetus (Fig 1.6): an amphibious whale with hind limbs
    3. Documenting the transition from land to water 1:  Isotopic analysis of fossil teeth (Fig. 1.9)
      1. Terrestrial animals drink freshwater; marine animals drink saltwater
      2. O18/O16 ratio higher in saltwater : Higher ratio in teeth of marine animals
    4. Documenting the transition from land to water 2: hindlimb loss
      1. Fossils document hindlimb loss (Fig. 1.11)
      2. Changes in gene expression led to hindlimb loss (Fig. 1.9)10
        1. Hindlimbs begin to form but do not fully develop
    5. Research gives more clues about whale evolution
      1. Loss of teeth in baleen whales
        1. Ancestors of all modern whales had teeth: Also produced small patches of baleen
        2. Baleen completely replaced teeth in Mysticetes: Genes for building teeth disabled
      2. Evolution of brain size and complexity (Fig. 1.12)
        1. the result of natural selection
        2. Sociality promoted the evolution of large brains; Form lasting alliances; Competition for mates; Complex communication 
      3. Whale diversity over evolutionary time (Fig. 1.13)
      1. Historical diversity tracks ecological changes to food web
      2. Small populations put some cetaceans at risk of extinction (Figs. 1.14-1.15)


Restoration of Ambulocetus from Wikipedia

Ambulocetus natans, a primitive whale from the Eocene of Pakistan, pencil drawing, digital coloring Date 29 October 2007 Source Own work Author Nobu Tamura (

Relationships of Cetacea (Artiodactyla) Among Mammals
Figure taken from Spaulding M, O'Leary MA, Gatesy J (2009) Relationships of Cetacea (Artiodactyla) Among Mammals: Increased Taxon Sampling Alters Interpretations of Key Fossils and Character Evolution. PLoS ONE 4(9): e7062. doi:10.1371/journal.pone.0007062

1.3 Evolution: A Tapestry of Concepts

  1. Natural Selection
    1. mechanism that can lead to evolution, whereby differential survival or reproduction of individuals causes some genetic types to replace (outcompete) others
    2. Mutation and Recombination
    3. Genetic Drift
    4. Phenotypes

  1. Experiments with mice demonstrate viral evolution (Fig. 1.20 from Hensley et al. 2009 Science )
    1. Figure from MIT Open Access article
  2. Viral reassortment can lead t

Common misconceptions about evolution (p. 24)
  • Misconceptions and lack of understanding about the theory of evolution are common, but evolution is not 'just a theory' that explains 'everything.'
  • Accepting evolution does not mean accepting a predetermined outcome for species diversity or human behavior.
  1. Evolution is 'just' a theory
    1. WRONG: Scientific theories backed by multiple lines of evidence.
      1. Provide overarching explanation for major aspects of natural world.
      2. Other scientific theories: Gravity, Plate tectonics, Germ theory
      3. Evolutionary theory is overwhelmingly accepted by scientists
  2. Evolutionary biologists understand everything about the history of life 
    1. WRONG: Biologists continually discover new aspects of life. All evidence fits within context of evolution
  3. Evolution explains the origin of life
    1. WRONG: Evolution deals with how life has changed after it originated. Other scientific fields address the origin of life
  4. Evolutionary biologists search for missing links
    1. WRONG: Biologists expect the fossil record to be incomplete
      1. Finding direct ancestors is unlikely
      2. Available evidence strongly supports relationships between current and past species
      3. Relationships shed light on how traits evolved
  5. Evolution violates the second law of thermodynamics (entropy)
    1. WRONG: 2nd law Holds that disorder increases in closed systems. Earth is not a closed system. Sun provides constant input of energy
  6. Evolution is natural selection
    1. WRONG: Natural selection is a mechanism of evolutionary change. Other mechanisms: Genetic drift, Sexual selection
  7. Evolution is entirely random
    1. WRONG: Evolution includes random and non-random components
      1. Mutations are random
      2. Natural selection is the non-random spread of particular mutations
      3. Convergent evolution demonstrates that evolution is non-random. Phenotypes are predictable when environments are similar
  8. Organisms evolve adaptations  they 'need'
    1. WRONG: Evolution cannot identify needs. Mutations do not occur because they would be adaptive in an environment. If beneficial mutations happen to occur they may increase in frequency through selection
  9. Evolution is a march of progress
    1. WRONG: Evolution is not ladder-like. New species result from branching events
  10. Evolution always moves from simple to complex
    1. WRONG: Evolution can also move from complex to simple. E.g. mitochondria evolved from free-living bacteria
  11. Evolution results from individuals adapting to environment
    1. WRONG: Evolution only works on inherited traits. Acquired changes are not passed to offspring
    2. Populations evolve; individuals do not. Evolution results from changes in allele frequencies
  12. Organisms are perfectly adapted to their environment
    1. WRONG: Natural selection can only work with available variation . Constrained by physics and development. Many traits involved in trade-offs, e.g. human brain size
  13. Evolution happens for the good of the species
    1. WRONG: Evolution selects traits that are beneficial for individuals or their genes. Traits that are bad for individuals (or genes) will not be selected even if they are good for the species
  14. Evolution promotes selfishness and cruelty
    1. WRONG: Natural selection favors traits that increase reproductive success. Different conditions select for different traits. Cooperative traits are beneficial under some conditions
  15. Evolution seeks peaceful harmony in nature
    1. WRONG: Natural selection favors traits that increase reproductive success. Can result in exploitation
  16. Life can be divided into higher and lower forms
    1. WRONG: All of life is adapted to the environment in numerous ways. Environments differ so adaptations differ. One adaptation is not 'superior' to another adaptation
  17. Evolution has produced a stable diversity of life
    1. WRONG: Extinction means diversity is not stable. Around 99% of all species that ever existed are extinct


  1. Natural Selection Acts on Individuals, but Its Consequences Occur in Populations
    1. individuals and their genes are not modified; selection determines which genes will survive
  2. Natural Selection Acts on Phenotypes, but Evolution Consists of Changes in Gene Frequencies
    1. unless the genotype frequency changes there is no evolution 
    2. If variation is due to differences in genotype, then the survivors of selection pass their successful phenotypes to their offspring.
  3. Natural Selection is Backward, Not Forward Looking
    1. each generation is the result of selection on the previous generation
  4. Natural Selection Can Produce New Traits, Even Though It Acts on Existing Traits
    1. selection works on variation already present.
    2. selection can lead to new characteristics by changing functions of preexisting traits, genes, etc. preadaptations, exaptions---the panda's thumb
  5. Natural Selection is Not Perfect
  6.  Natural Selection is Nonrandom, but It is not Progressive
    1. selection is not teleological, there is no conscious intent (either by the organism or a creator), but it does increase adaptation to the environment.
    2. evolution has tended to increase complexity, but some organisms have changed very little (e.g., bacteria) or become less complex (e.g., tapeworms).
    3. all life has evolved for the same amount of time--not higher or lower organisms
  7. Fitness is Not Circular
    1. fitness is testable, not a tautology (circular reasoning--those who survive)
    2. research can determine why certain nonrandom groups are favored
    3. fitness can be measured by counting offspring, observing which individuals survive selection events.
  8. Natural Selection Act on Individuals, Not Groups
    1. altruism does not occur in nature.
    2. behavior maximizes individual fitness

Is there necessarily a conflict between evolutionary biology and religion?

  1. Methodological naturalism
    1. As a scientist, regardless of other personal beliefs, hypotheses can only be framed in terms of natural causes
  2. Ontological naturalism (=metaphysical naturalism)
    1. The natural world is all there is




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