Lecture 11 Notes

Notes on Lecture 11

(organized by theme, rather than lecture slides)

Evolution (Slides 3, 4)

Evolution is a mechanism that explains genotypic and phenotypic changes

  • It's important because:
    • the diversity of life is a product of evolutionary processes, and driven by natural selection
    • evolution never ends. e.g. pest resistence to insecticides, the spread of transgenes
    • the constraints and opportunities for adaptation depend on evolutionary processes
    • we can act as an evolutionary agent of natural selection. e.g. over-harvesting of large fish can result in fish having smaller body sizes and can affect their growth rates
    • In order to be effective natural resource managers, we need to understand how evolutionary processes work
  • Definitions:
    • the change in the proportion of alleles (genetic composition) of a population over time (with the passage of each generation)
    • (Darwin) i) the gradual change of living things from one form into another over the course of time
    • (Darwin) ii) the origin of species and lineages by descent of living forms from ancestral forms, and the generation of diversity
    • i) relates to microevolution, ii) relates to macroevolution. Macroevolution is a scaled up version of microevolution
    • Darwin didn't have genetics to draw upon so he thought about evolution in terms of ii)

History of Evolutionary Thought (Slides 5 - 14)

Contributors to Evolutionary Thought

  • Carl Linnaeus
    • Swedish Botanist, famous for his taxonomic system (creating binomial nomenclature!) for organisms,
    • based taxonomic delineations on the presence of similar characteristics among organisms (nested classifications)
  • Hutton
    • Geologist, promoted the concept of gradualism (small changes occurring over a long period of time can create large changes)
  • Lamarck
    • posited an incorrect mechanism for evolution (transmutation), argued that the physical changes in organisms occur overtime
  • Virey
    • proposed that the term "evolution" be used to denote transmutation in species in 1816
    • a full 43 years before Darwin published his book on the origin of species!
  • Malthus
    • argued populations grow exponentially, individuals will compete with each another for resources
    • overpopulation leads to famine, disease, excess individual mortality
  • Cuvier
    • pioneer of paleontology
    • he showed that extinctions were common
  • Charles Lyell
    • Uniformitarianism "the present is the key to the past"
    • the processes operating today (e.g. deposition, wind) can provide explanations for past changes on earth.
  • A.R. Wallace
    • independently developed natural selection based on his travels around the world
    • (more modest origins than Darwin - who was a gentleman), made a living as a collector of rare organisms, wrote an essay to Darwin
    • hastened Darwin's publication of Origin of Species, joint-presented the theory of natural selection with C. Darwin
  • Erasmus Darwin - grandfather of Charles Darwin
    • considered species to be changeable
  • Charles Darwin
    • posited the theory of natural selection as a mechanism to explain how evolution is driven
    • given the intellectual climate of the day, Prof. Allan suggests, "This idea was ripe for the taking."

Other Concepts Shaping the Intellectual Climate of the Day

  • People understood artificial selection (e.g. pigeon breeding, horse breeding, dog breeding)
  • fossil discoveries revealed life forms previously unknown (T. Jefferson was a fossil collector)
  • people knew about strata
  • similarities among organisms (Linnaeus) were beginning to be seen as evidence of relatedness

Evolution revolutionized how we thought of our place in the universe (Slide 5)

Darwin's contributions (Slides 11 - 17)

Darwin's Voyage on the Beagle

  • Darwin was 22 when he left on voyage as naturalist; returned when he was 27
  • Spent a great deal of time on the Galapagos Islands and observed finches with differing beak sizes
  • documented of his observations of natural selection from his voyage, developed ideas of natural selection, sexual selection,
  • two years after his voyage, Darwin's theory of evolution was developed, but he waited to publish as he was worried about the consequences.

The Logic Behind Darwin's Natural Selection

  1. Individuals produce more offspring than are required for replacement (Malthus)
  2. Individuals vary in physical and behavioural traits (observation from the Beagle)
  3. Many traits are heritable (Mendel's work with peas)
  4. Individuals holding traits that benefit survival and reproduction will pass those traits to a greater proportion of the future generation

Natural Selection requires:

  • genetic variation that's inheritable
  • different alleles (or forms) of an inheritable trait have different probabilities of survival and/or reproduction in a given environment

Evolution as a Full Theory

  • Organisms have changed over time. Those living today are different from those that lived in the past.
  • All organisms are derived from common ancestors via a process of branching. Similarities of traits are evidence of a recent, common ancestor.
  • Change is gradual and slow, requiring a very long time.
  • Natural selection is the main driving mechanism of evolutionary change.
  • Over time, branching of species generates the entire tree of life

Darwin's Dangerous Idea

  • human evolution is affected by the same natural processes as other organisms
  • evolution does not push organisms toward an ideal form
  • humans are not the pinnacle of evolution

Types of Natural Selection (Slides 19 - 25)

  • Stabilizing selection aka Goldilocks Selection
    • there's a range of traits (in the graph on slide 20, it shows a normal distribution)
    • the average trait is the most fit, such that the extreme traits at both tails are lost
    • this results in a more narrow distribution and a higher number of individuals with the average trait
    • e.g. fur color in mice: individuals that are too pale or too dark are less fit than individuals with "the right mix"
    • e.g. Babies of intermediate birth weight have higher survivorship than very small and very large babies
  • Directional selection
    • again, a range of traits is shown as a normal distribution
    • change occurs in one direction, changing from one phenotype to another
    • this results in changes over time (macroevolution?)
    • e.g. giraffe necks, directional selection from short to long, big and strong :), male giraffes with longer necks have an advantage when fighting with other males, but a disadvantage when trying to drink water (possibly limiting the amount of directional selection that can occur)
    • e.g. horse fossil records: over time, horses grew taller, started living in open savannahs, hoof evolved from the nail of third digit (used to have long feet), adapted grazing: from leafy vegetation to grass, evolution is related to environmental changes (wet —> dry; leafy vegetation —> grass)
    • e.g Peppered moth example.
  • Disruptive selection
    • start with a normal distribution, two extremes on either side are more fit, causing the average to be less fit, and two peaks to develop within the distribution
    • this is a possible mechanisms for speciation without environmental barriers (sympatric speciation)
    • e.g. beaks selecting for hard or soft seeds, pushes them into two different morphotypes

Genetic Variation (Slides 26 - 35)

What Maintains Genetic Variation in Populations?

  • Mutation
  • Migration
  • Environmental Variation
  • Sex
  • Trade-offs

Prof. Allan argues that environmental variation, sex and trade-offs are the most important


  • the ultimate source of all genetic variation
  • mutations are most often deleterious
  • do not arise out of need
  • number of mutations: 10^-5 - 10^-6 per locus, so each person has, on average, 1 - 2 mutations in their genotype


  • exchange of individuals among discrete populations
  • may introduce novel traits
  • Allan argues migration has a small impact BUT …
  • migration among sub-populations is important for the maintenance of genetic diversity and population size, which, in turn, can allow a population to persist (allowing for more time for evolutionary diversification and decreasing the probability of extinction over time)

Sex - value and cost

  • during meiosis, chromosomes from the female and male gamete recombine, so that gametes have different combinations of their parents' chromosomes
  • during meiosis, individual chromosomes can "cross-over", so that gametes have chromosomes that are unique mixtures of their parents' chromosomes
  • Therefore, sexual reproduction results in gametes that are genetically unique, with novel genotypes
  • Some genotypes are more fit than others
  • lineages that are able to do sexual reproduction will outlast ones that cannot

Alternative to Sex: Clonal Reproduction

  • with the exception of changes due to mutations, all genotypes are identical
  • good in short run, not good when there's environmental variability, or if there's a fast environmental change
  • some species can do both sexual and clonal reproduction

Environmental Variation

  • when natural selection favors different genotypes in different years or locations
  • "directional selection that keeps changing its mind"
  • e.g. rapid evolution of beak size in Darwin's finches:
    • drought causes the number of seeds to crash, resulting in a large drop in the number of finches
    • Some years there are only large, hard seeds available, so birds with large beaks can crack them better and thus survive better.
    • other years, more small seeds are available, and small birds with small beaks survive better.


  • Energy expended developing one character trait not available for something else
  • Can allocate resources to growth or reproduction, but not both
  • Cannot be "perfect" at everything

e.g. Douglas Fir

  • Tradeoff between growth rate and cones per tree (reproduction)
  • grow fast or reproduce more (might be equally good alternatives).

e.g. Guppies in Trinidad ( Slides 34 - 37)

  • famous transplant study performed in area of coarse topography with steppe streams
  • guppy size, coloration and behaviour are affected by the presence of predators
  • Predators: pike-cichlids (prey on larger guppies), killifish (prey on small guppies)
  • in some of pools above waterfalls with killifish, female guppies are bigger and have a later age of maturity
    • IOW: guppies escape predation by getting larger faster and delaying reproduction until they are no longer the ideal size for killifish
  • in pools with pike-cichlids, female guppies are smaller and have an earlier age of maturity
  • This shows that organisms may have equal fitness but allocate resources in different ways.


a. Evolution is change in the genetic composition of a population with passage of each generation
b. Natural selection is primary mechanism, requiring heritable variation and differential survival and reproduction
c. Selection can be stabilizing, disruptive or directional
d. Genetic variation originates through mutation and is maintained by sexual recombination, environmental variation, tradeoffs (and migration)

Other kinds of evolution

- Genetic drift
- movement of organisms
- artificial selection
- genetic engineering

Hardy-Weinberg Equilibrium (Slide 41)

  • this is a tool to understand selection and drift
  • Equation: p^2 + 2pq + q^2 = 1
  • Equation 2: p + q = 1 (if only 2 alleles)

When is a population not evolving (i.e. when in H-W equilibrium)?

1) when there's an infinitely large population
2) when there's random mating
3) when there's no migration
4) when there's no selection
5) when there's no mutation

Deviations from the Hardy-Weinberg equilibrium

1) Small populations

  • genetic drift
    • by chance, some alleles are more likely to be lost and others more likely to be fixed in a small population
  • bottleneck, founder effects
    • catastrophic mortality leading to only a few survivors
    • by chance, these small populations become more genetically similar, lose heterozygosity
    • e.g. bottleneck: Cheetahs are homozygous at many loci, skin grafts will "take" between different individuals
  • genetic drift is a problem that small populations often face (conservation problem)
  • Really small populations living in habitat fragments by chance alone, genetic variation can disappear.

4) Directional Selection (Slide 42)

  • e.g. Humans have been selecting organisms for thousands of years via artificial selection
  • e.g. Fishing: harvesting large fishes means survivors reproduce at smaller size and younger age


Definition: the number of offspring produced over an individual's lifetime that survive to reproduce (counted as children "F1" or grandchildren "F2")

Estimating Fitness (Slides 47 - 49, with some additions from a quick scan of the internets)

  • Absolute Fitness the potential for individuals of genotype X to survive and reproduce given current selective pressures.
    • W(abs) = (# individuals with a genotype X after selection)/(# individuals with genotype X before selection)
  • Relative Fitness the potential for individuals of genotype X to survive and reproduce given current selective pressures, as compared to the average fitness of the entire population.
    • W(rel) = (avg # of surviving progeny of genotype X)/(avg # of surviving progeny of competing genotypes) after a single generation
    • can also be estimated from life tables as: (# individuals surviving to adult stage) x (fecundity of survivors)
  • Fitness (W) = 1 when each parent is represented by one reproducing offspring in the next generation
  • W>1 = more fit parents, W < 1 = less fit parents
  • Offspring of more fit parents will eventually dominate the population.

There are no perfect phenotypes (Slide 50)

  • Evolution by natural selection does act to maximize fitness, but all organisms are not maximally fit because of:
    • Phylogenetic constraints (nature's inertia: there's a limit to how much a species can evolve given the basic body plan that has already evolved)
    • Environmental variation (selective pressures change over time)
    • Trade-offs (e.g. can maximize reproduction or growth, but not both)


  • the term for fitness, W, is completely relative to others in the population and the current environment (IOW: W measures how well you do in this particular ecosystem compared to others in that system)

How does altruism evolve? (Slide 53)

  • Darwin thought this was a problem that could undermine the whole theory of natural selection
  • posited the idea of Kin Selection to explain altruism:
      • Selection may favour traits that decrease the fitness of an individual but increase the reproductive success of close relatives

Hamilton's Inequality (Slide 55)

  • William Hamilton (1964) showed that an altruistic allele could increase in frequency when

relatedness*benefit - cost>0
(rb - c>0)

  • relatedness (r) = proportion of alleles in two individuals that are identical by descent
  • for full siblings, r = 0.5

Inclusive fitness (Slide 55)

  • includes direct fitness + indirect fitness
  • Direct fitness personal reproduction
  • Indirect fitness additional reproduction of relatives made possible by an individual's action

Inclusive Fitness: When do we cooperate?

  • if genes for traits shared by relatives and looking after relatives contributes to survival of your genes
  • selection acts upon the gene, as opposed to the individual (Dawkins: The Selfish Gene)

examples of altruism:
ground squirrels

  • most alarm calling done by adult females, adult males do not call, juvies don't call
  • who's benefiting?
  • those females are more likely to call if daughters, mothers, or litter-mate sisters are in the vicinity

white-fronted bee eaters

  • young adults forgo reproduction in order to help look after juveniles of close relatives
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