Chapter 21 Genes within populations

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Chapter 21Genes within populations
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Question?

• How did the diversity of life originate?
• Through the process of Evolution.

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Evolution

• The processes that have transformed life on earth
  from its beginnings to today's diversity.
• Evolution is the most pervasive principle in
  biology.

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Theory vs theory

• Hypothesis supported repeatedly by data.
• Makes testable predictions

• Laypersons definition.
• Confused with hypothesis in Science.

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Examples of Theory

• Cell Theory
• Big Bang Theory
• Atomic Theory
• Theory of Gravity
• Theory of Evolution

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Teaching Philosophy on Evolution
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Evolution

• Has itself "evolved" or changed over time.
• Illustrates Science as a Process.
• Students should be able to give the main points
  of several views.

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Pre-Darwinian Views

• 1. Greeks
• 2. Fixed Species
• 3. Catastophism
• 4. Hutton and Lyell
• 5. Lamarck

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Greek Philosophers

• 1. Plato - Organisms are already perfectly
  adapted to their environments.
• 2. Aristotle - Organisms arranged on a scale of
  life from simple to complex.

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Result

• No evolution.
• Life is already perfect and doesnt need to
  change. All the rungs on life's "ladder"
  are already occupied.

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Fixed Species Concept

• The creator had designed each and every species
  for a particular purpose.

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Result

• No evolution.
• Created the viewpoint that all species could be
  identified and named (Taxonomy). A major
  factor in the Linnaeus classification system.

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Catastrophism

• Georges Cuvier (1769-1832).
• Attempted to relate fossils to current life.

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Theory

• Fossils were the remains of species lost due to
  catastrophe.
• No new species originated species could only be
  lost over time.
• Result - No evolution.

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James Hutton

• 1795 - Gradualism
• Profound change is the cumulative product of
  slow, but continuous processes.

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Result

• Changes on the earth were gradual, not
  catastrophic.

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Charles Lyell

• 1797 - 1875.
• Incorporated Huttons gradualism into a theory
  called Uniformitarianism.

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Uniformitarianism

• Geological processes have operated at the same
  rate over the Earths history.

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Result

• The Earth must be VERY old. (much older than 6000
  years of the fixed species concept).
• Idea that slow and subtle processes can cause
  substantial change.

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Jean Baptiste Lamarck

• Published theory in 1809.
• Theory - Life changed from simple to complex over
  time.

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Lamark

• Fossils were the remains of past life forms.
• Evolution did occur.

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Mechanisms

• 1. Use and Disuse -
• Body parts used to survive become larger and
  stronger.
• Body parts not used to survive deteriorate.

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Mechanisms

• 2. Acquired Characteristics
• Modifications acquired by use/disuse were passed
  on to offspring.

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Problem

• No knowledge of genetics.
• Acquired traits are not transmitted offspring.

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Lamarcks Credits

• Did suggest correctly the role of fossils in
  evolution.
• Did suggest that adaptation to the environment is
  a primary product of evolution.

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Charles Darwin

• Father of the modern theory of evolution.
• Theory - Descent with Modification.

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Darwin's Background

• Trained as a Naturalist (after trying religion
  and medicine).

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Voyage of the Beagle
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Result

• Darwin's training and travel opportunities
  allowed him to formulate and support his ideas on
  Natural Selection.

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Galapagos Finches
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Alfred Wallace - 1858

• Paper on Natural Selection identical to Darwin's
  ideas.

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Result - July 1, 1858

• Dual presentation of the Wallace-Darwin ideas to
  the Linnaean Society of London.

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Darwin - 1859

• Publication of "The Origin of Species

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Comment

• Darwin best remembered for the theory because of
  his overwhelming evidence and because he
  published.

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Darwinian View

• History of life is like a tree with branches over
  time from a common source.
• Current diversity of life is caused by the forks
  from common ancestors.

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Example
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The Origin of Species

• Documented the occurrence of evolution.
• Suggested that the mechanism for evolution was
  Natural Selection.

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The Facts

• Fact 1 - All species reproduce
  themselves exponentially.

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• Fact 2 - Most populations are normally stable in
  size.
• Fact 3 - Natural Resources are limited (finite).

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Inference 1

• The large number of offspring must compete for
  the finite resources.
• Result - Most offspring die.

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Thomas Malthus

• Essay on human population growth in 1798.
• Disease, famine, homelessness, and war are
  inescapable because human populations grow faster
  than food supplies.
• Darwin read Malthus.

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More Facts

• Fact 4 - No two individuals in a population are
  exactly alike.
• Fact 5 - Variation is inheritable.

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Inference 2

• Those individuals whose inherited characteristics
  fit them best to their environment survive and
  reproduce.

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Inference 3

• Offspring inherit the favorable characteristics.
  Populations shift over time as the favorable
  characteristics accumulate.

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Nature

• Determines which characteristics are favorable.
• Determines who survives.
• Result - Natural Selection

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Artificial Selection

• When man determines the characteristics that
  survive and reproduce.
• Result - the various breeds of animals and plants
  weve developed.

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Ex - Mustard Plant

• Original

• Cultivars

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Evolution Success Measured By

• Survival
• Reproduction
• Whoever lives long enough and has kids is the
  winner in evolution.

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Requirements

• In order for Natural Selection to work, you must
  have
• Long periods of time.
• Variations within a population.

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Subtleties of Natural Selection

• 1. Populations are the units of Evolution.
• 2. Only inherited characteristics can evolve.

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Comment

• Acquired characteristics may allow a species to
  evolve "outside" of Natural Selection.
• Ex culture, learning

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Additional Signs

• 1. Biogeography
• 2. Fossils
• 3. Taxonomy
• 4. Comparative Anatomy
• 5. Comparative Embryology
• 6. Molecular Biology

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Biogeography

• The geographical distribution of species.
• Problem
• Species mixtures on islands
• Marsupials in Australia

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Evolution Viewpoint

• Biogeographical patterns reflect descent from the
  ancestors that colonized that area.

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Fossils

• Relics or impressions of organisms from the past.
• Problem
• Show changes over time from simple to complex.
• Many fossils don't have descendants.

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Evolution Viewpoint

• Life has changed over time.
• Many species failed to survive and became extinct.

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Comments

• 1. Fossilization is a rare event.
• 2. Only hard parts fossilize well.
• 3. Problem in finding fossils.
• 4. Interpretation.
• 5. Missing Links.

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Taxonomy

• Science of Classification.

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Main Categories

• Domain
• Kingdom
• Phylum or Division
• Class
• Order
• Family
• Genus
• Species

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• Problem - Why can life be grouped this way?
• Evolution Viewpoint -Hierarchy reflects the
  branching genealogy of the tree of life.

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Question?

• Is the unit of evolution the individual or the
  population?
• Answer while evolution effects individuals, it
  can only be tracked through time by looking at
  populations.

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So what do we study?

• We need to study populations, not individuals.
• We need a method to track the changes in
  populations over time.
• This is the area of Biology called population
  genetics.

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Population Genetics

• The study of genetic variation in populations.
• Represents the reconciliation of Mendelism and
  Darwinism.

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Modern Synthesis

• Uses population genetics as the means to track
  and study evolution.
• Looks at the genetic basis of variation and
  natural selection.

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Population

• A localized group of individuals of the same
  species.

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Species

• A group of similar organisms.
• A group of populations that could interbreed.

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Gene Pool

• The total aggregate of genes in a population.
• If evolution is occurring, then changes must
  occur in the gene pool of the population over
  time.

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Microevolution

• Changes in the relative frequencies of alleles in
  the gene pool.

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Hardy-Weinberg Theorem

• Developed in 1908.
• Mathematical model of gene pool changes over time.

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Basic Equation

• p q 1
• p dominant allele
• q recessive allele

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Expanded Equation

• p q 1
• (p q)2 (1)2
• p2 2pq q2 1

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Genotypes

• p2 Homozygous Dominants2pq Heterozygousq2
  Homozygous Recessives

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Example Calculation

• Lets look at a population where
• A red flowers
• a white flowers

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Starting Population

• N 500
• Red 480 (320 AA 160 Aa)
• White 20
• Total Genes 2 x 500
  1000

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Dominant Allele

• A (320 x 2) (160 x 1)
• 800
• 800/1000
• A 80

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Recessive Allele

• a (160 x 1) (20 x 2)
• 200/1000
• .20
• a 20

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A and a in HW equation

• Cross Aa X Aa
• Result AA 2Aa aa
• Remember A p, a q

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Substitute the values for A and a

• p2 2pq q2 1
• (.8)2 2(.8)(.2) (.2)2 1
• .64 .32 .04 1

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Dominant Allele

• A p2 pq
• .64 .16
• .80
• 80

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Recessive Allele

• a pq q2
• .16 .04
• .20
• 20

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Result

• Gene pool is in a state of equilibrium and has
  not changed because of sexual reproduction.
• No Evolution has occurred.

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Importance of Hardy-Weinberg

• Yardstick to measure rates of evolution.
• Predicts that gene frequencies should NOT change
  over time as long as the HW assumptions hold (no
  evolution should occur).
• Way to calculate gene frequencies through time.

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Example

• What is the frequency of the PKU allele?
• PKU is expressed only if the individual is
  homozygous recessive (aa).

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PKU Frequency

• PKU is found at the rate of 1/10,000 births.
• PKU aa q2
• q2 .0001
• q .01

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Dominant Allele

• p q 1
• p 1- q
• p 1- .01
• p .99

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Expanded Equation

• p2 2pq q2 1
• (.99)2 2(.99x.01) (.01)2 1
• .9801 .0198 .0001 1

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Final Results

• Normals (AA) 98.01
• Carriers (Aa) 1.98
• PKU (aa) .01

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AP Problems Using Hardy-Weinberg

• Solve for q2 ( of total).
• Solve for q (equation).
• Solve for p (1- q).
• H-W is always on the national AP Bio exam (but no
  calculators are allowed).

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Hardy-Weinberg Assumptions

• 1. Large Population
• 2. Isolation
• 3. No Net Mutations
• 4. Random Mating
• 5. No Natural Selection

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If H-W assumptions hold true

• The gene frequencies will not change over time.
• Evolution will not occur.
• But, how likely will natural populations hold to
  the H-W assumptions?

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Microevolution

• Caused by violations of the 5 H-W assumptions.

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Causes of Microevolution

• 1. Genetic Drift
• 2. Gene Flow
• 3. Mutations
• 4. Nonrandom Mating
• 5. Natural Selection

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Genetic Drift

• Changes in the gene pool of a small population by
  chance.
• Types
• 1. Bottleneck Effect
• 2. Founder's Effect

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By Chance
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Bottleneck Effect

• Loss of most of the population by disasters.
• Surviving population may have a different gene
  pool than the original population.

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Result

• Some alleles lost.
• Other alleles are over-represented.
• Genetic variation usually lost.

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Importance

• Reduction of population size may reduce gene pool
  for evolution to work with.
• Ex Cheetahs

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Founder's Effect

• Genetic drift in a new colony that separates from
  a parent population.
• Ex Old-Order Amish

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Result

• Genetic variation reduced.
• Some alleles increase in frequency while others
  are lost (as compared to the parent population).

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Importance

• Very common in islands and other groups that
  don't interbreed.

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Gene Flow

• Movement of genes in/out of a population.
• Ex
• Immigration
• Emigration

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Result

• Changes in gene frequencies within a population.
• Immigration often brings new alleles into
  populations increasing genetic diversity.

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Mutations

• Inherited changes in a gene.

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Result

• May change gene frequencies (small population).
• Source of new alleles for selection.
• Often lost by genetic drift.

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Nonrandom Mating

• Failure to choose mates at random from the
  population.

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Causes

• Inbreeding within the same neighborhood.
• Assortative mating (like with like).

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Result

• Increases the number of homozygous loci.
• Does not in itself alter the overall gene
  frequencies in the population.

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Natural Selection

• Differential success in survival and
  reproduction.
• Result - Shifts in gene frequencies.

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Comment

• As the Environment changes, so does Natural
  Selection and Gene Frequencies.

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Result

• If the environment is "patchy", the population
  may have many different local populations.

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Genetic Basis of Variation

• 1. Discrete Characters Mendelian traits with
  clear phenotypes.
• 2. Quantitative Characters Multigene traits
  with overlapping phenotypes.

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Polymorphism

• The existence of several contrasting forms of the
  species in a population.
• Usually inherited as Discrete Characteristics.

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Examples

• Garter Snakes

• Gaillardia

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Human Example

• ABO Blood Groups
• Morphs A, B, AB, O

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Other examples
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Quantitative Characters

• Allow continuous variation in the population.
• Result
• Geographical Variation
• Clines a change along a geographical axis

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Yarrow and Altitude
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Sources of Genetic Variation

• Mutations.
• Recombination though sexual reproduction.
• Crossing-over
• Random fertilization

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Preserving Genetic Variation

• 1. Diploidy - preserves recessives as
  heterozygotes.
• 2. Balanced Polymorphisms - preservation of
  diversity by natural selection.

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Example

• Heterozygote Advantage - When the heterozygote or
  hybrid survives better than the homozygotes.
  Also called Hybrid vigor.

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Result

• Can't bred "true and the diversity of the
  population is maintained.
• Ex Sickle Cell Anemia

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Comment

• Population geneticists believe that ALL genes
  that persist in a population must have had a
  selective advantage at one time.
• Ex Sickle Cell and Malaria, Tay-Sachs and
  Tuberculosis

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Fitness - Darwinian

• The relative contribution an individual makes to
  the gene pool of the next generation.

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Relative Fitness

• Contribution of one genotype to the next
  generation compared to other genotypes.

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Rate of Selection

• Differs between dominant and recessive alleles.
• Selection pressure by the environment.

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Modes of Natural Selection

• 1. Stabilizing
• 2. Directional
• 3. Diversifying
• 4. Sexual

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Stabilizing

• Selection toward the average and against the
  extremes.
• Ex birth weight in humans

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Directional Selection

• Selection toward one extreme.
• Ex running speeds in race animals.
• Ex. Galapagos Finch beak size and food source.

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Diversifying

• Selection toward both extremes and against the
  norm.
• Ex bill size in birds

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Comment

• Diversifying Selection - can split a species into
  several new species if it continues for a long
  enough period of time and the populations dont
  interbreed.

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Sexual Mate selection

• May not be adaptive to the environment, but
  increases reproduction success of the individual.
• This is a VERY important selection type for
  species.

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Result

• Sexual dimorphism.
• Secondary sexual features for attracting mates.

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Comments

• Females may drive sexual selection and dimorphism
  since they often "choose" the mate.

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Question

• Does evolution result in perfect organisms?

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Answer - No

• 1. Historical Constraints
• 2. Compromises
• 3. Non-adaptive Evolution (chance)
• 4. Available variations most come from using a
  current gene in a new way.

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Summary

• Know the difference between a species and a
  population.
• Know that the unit of evolution is the population
  and not the individual.

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Summary

• Know the H-W equations and how to use them in
  calculations.
• Know the H-W assumptions and what happens if each
  is violated.

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Summary

• Identify various means to introduce genetic
  variation into populations.
• Know the various types of natural selection.

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Summary

• Darwin's ideas now a "Theory.
• Predictions of a Theory are tested by experiments
  and observations.
• Be familiar with the pre-Darwin views of
  evolution.