Organic%20Evolution

1
Organic Evolution

• Chapter 6

2
Evolution - Defined

• Evolution a change in the genetic composition
  of a population over time.
• A change in the frequency of certain alleles.
• On a larger scale, evolution can be used to refer
  to the gradual appearance of all biological
  diversity.

3
Darwins Revolutionary Theory

• The Origin of Species focused attention on the
  diversity of life, similarities as well as
  differences, and the adaptations organisms have
  for particular environments.

4
Darwins Revolutionary Theory

• Charles Darwin presented evidence that many
  modern organisms are descended from ancestral
  species that were different.

5
Darwins Revolutionary Theory

• Prevailing view of the world was that the Earth
  was only a few thousand years old and that all
  life had been created at the beginning and
  remained unchanged.

6
Pre-Darwinian Evolutionary Ideas

• Several ancient Greek philosophers thought life
  changed through time.
• Aristotle recognized fossils as forms of ancient
  life.
• He developed the scala naturae (scale of nature).
  
• Each form of life had a rung on the ladder.
• Organisms were arranged in order of complexity.
• The ancient Greeks didnt propose an evolutionary
  mechanism.

7
Pre-Darwinian Evolutionary Ideas

• Lamarck was the first to suggest an explanation
  for evolution.
• Inheritance of acquired characteristics
• Didnt hold up to testing.

8
A Mechanism for Evolution

• Darwin presented a mechanism for evolution
  natural selection.
• Organisms that are in some way more successful at
  reproduction will pass on more of their genes.
• Over time the traits responsible for that success
  will become widespread in the population.
• This theory holds up very well!!

9
Alfred Russell Wallace

• Wallace independently developed a theory of
  natural selection.
• He sent his manuscript to Darwin, spurring him to
  finally publish his ideas.
• Both ideas were presented to the Linnean Society
  in 1858.
• Darwin finished On the Origin of Species and
  published it in 1859.

10
Uniformitarianism

• Charles Lyells principle of uniformitarianism
• Laws of physics chemistry present throughout
  history of Earth.
• Past geological events similar to todays events.
• Principles of Geology

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Uniformitarianism

• Natural forces could explain the formation of
  fossil-bearing rocks.
• Lyell concluded the age of the earth must be
  millions of years.
• He stressed the gradual nature of geological
  changes.

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Uniformitarianism and the Age of Earth

• Darwin studied the work of Lyell closely. He
  took the first volume of Lyells Principles of
  Geology on the Beagle. He received the second
  volume while on the voyage.
• He concluded that Earth must be much older than
  6000 years.
• Perhaps these slow changes could work on living
  things as well..

13
Evolution in Need of a Mechanism

• Darwin was not the first to have the thought that
  organisms change through time.
• His grandfather, Erasmus Darwin, and others
  suggested that life evolves as environments
  change.
• But a mechanism for that change was needed.

14
Darwin (1809 1882)

• Darwin had a lifelong love of nature.
• His father wanted him to study medicine.
• This was not what Darwin wanted and he didnt
  finish.

15
Darwin

• After leaving medical school he attended
  Cambridge University with the intention of
  entering the clergy.
• His mentor and botany professor, John Henslow,
  recommended him for a position as ships
  naturalist aboard the Beagle.

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The Voyage of the Beagle

• Darwin started out on a five year trip around the
  world aboard the Beagle in 1831. He was 22.
• As ships naturalist he spent his time on shore
  collecting thousands of plant and animal
  specimens and making important observations.

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The Voyage of the Beagle

• Darwin saw that the plants and animals that he
  found in temperate areas of South America were
  more similar to tropical South American species
  than they were to temperate European species.

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The Voyage of the Beagle

• The fossils he found in South America were more
  like modern South American species than European
  species.

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The Voyage of the Beagle

• During the voyage he read Lyells Principles of
  Geology.
• He had Lyells ideas in mind as he traveled and
  observed the geology of South America.

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The Voyage of the Beagle

• He experienced an earthquake in Chile and
  observed that the coastline had risen several
  feet.
• He also found marine fossils high in the Andes
  Mountains.
• Darwin concluded that the mountains were formed
  by a series of such earthquakes.

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The Voyage of the Beagle

• Darwin became interested in the geographic
  distribution of organisms after visiting the
  Galapagos Islands.

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After the Voyage

• After returning, Darwin realized that adaptation
  to the environment and the origin of new species
  were closely linked processes.
• Galapagos finch species have evolved by adapting
  to specific conditions on each island.

23
Natural Selection

• After reading a paper by Thomas Malthus
  concerning the fact that human populations
  increase faster than limited food resources,
  Darwin noticed the connection between natural
  selection and this ability of populations to
  overreproduce.

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Natural Selection

• Only a small fraction of all offspring produced
  by any species actually reach maturity and
  reproduce.
• Natural populations normally remain at a constant
  size.

25
Natural Selection

• Those that survive may have heritable traits that
  increased their chances of survival.
• They will pass those traits on.
• The frequency of those traits will increase.

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Artificial Selection

• Artificial selection people selectively breed
  organisms with desired traits.
• Darwin noticed that considerable change can be
  achieved in a short period of time.

27
Natural Selection

• Natural selection occurs when organisms with
  particular heritable traits have more offspring
  that survive reproduce.

28
Natural Selection

• Natural selection can increase the adaptation of
  an organism to its environment.

29
Natural Selection

• When an environment changes, or when individuals
  move to a new environment, natural selection may
  result in adaptation to the new conditions.
• Sometimes this results in a new species.

30
Natural Selection

• Individuals do not evolve populations evolve.
• Evolution is measured as changes in relative
  proportions of heritable variations in a
  population over several generations.

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Natural Selection

• Natural selection can only work on heritable
  traits.
• Acquired traits are not heritable and are not
  subject to natural selection.

32
Natural Selection

• Environmental factors are variable.
• A trait that is beneficial in one place or time
  may be detrimental in another place or time.

33
Darwinian Evolutionary Theory Evidence

• The main premise underlying evolutionary theory
  is that the living world is always changing.
• Perpetual change in form diversity of organisms
  over the last 700 million years can be clearly
  seen in the fossil record.

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Fossils

• Fossils are remnants of past life preserved in
  the earth.
• Complete remains insects in amber.
• Petrified skeletal parts infiltrated with silica
  or other minerals.
• Or traces of organisms such as molds, casts,
  impressions, trackways, or fossilized excrement.

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The Fossil Record

• Fossils provide support for the idea that life
  changes through time.
• Fossil intermediates
• Whales descended from land mammals.
• Birds descended from one branch of dinosaurs.
• The oldest fossils are of prokaryotes.

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Dating Fossils

• Geological time can be measured in sedimentary
  rock layers.
• The Law of Stratigraphy
• Dates oldest layers at the bottom and youngest at
  the top.
• Time is divided into eons, eras, periods and
  epochs.

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Dating Fossils

• Radiometric dating methods are based on the decay
  of naturally occurring elements into other
  elements.
• Different methods used for different time periods.

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Dating Fossils - example

• 40K has a half life of 1.3 billion years
  meaning half of the 40K will have decayed to 40Ar
  and 40Ca. Half of what remains will decay in the
  next 1.3 billion years.
• Measure ratio of remaining 40K to the amount of
  40K originally there (remaining 40K plus 40Ar and
  40Ca).

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Fossil Record

• The fossil record of macroscopic organisms begins
  in the Cambrian period 505570 MYA.
• Fossil bacteria and algae, casts of jellyfishes,
  sponges spicules, soft corals, and flatworms are
  found in Precambrian rocks.
• Mostly microscopic

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Evolutionary Trends

• The fossil record shows that species arise and go
  extinct repeatedly throughout geological history.
• Trends appear in the fossil record directional
  changes in features or patterns of diversity.

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Evolutionary Trends

• The evolution of horses from the Eocene epoch
  (57.8 MYA) to the present is a well studied
  trend.
• Body size increasing
• Foot structure fewer toes
• Tooth structure larger grinding surface

42
Common Descent

• Darwin proposed that all organisms have descended
  from a single ancestral form.
• Life history is shown as a branching tree called
  a phylogeny.

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Homology

• The phrase descent with modification summarizes
  Darwins view of how Evolution works.
• All organisms descended from common ancestor.
• Similar species have diverged more recently.
• Homology when similar structures result from
  shared ancestry.

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Anatomical Homologies

• Homologous structures variations on a
  structural theme that was present in a common
  ancestor.
• Example vertebrate forelimbs have different
  functions, but share the same underlying
  structure.

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Anatomical Homologies

• Vertebrate embryos have a tail and pharyngeal
  pouches.
• These structures develop into different but
  homologous structures in adults.
• Gills in fishes
• Part of ears throat in humans.

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Ontogeny Phylogeny

• There are many parallels between ontogeny (an
  individuals development) and phylogeny
  (evolutionary descent).
• Embryological similarities
• Features of an ancestors ontogeny can be shifted
  earlier or later in a descendant's ontogeny.

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Ontogeny Phylogeny

• Heterochrony evolutionary change in timing of
  development.
• Characteristics can be added late in development
  and features are then moved to an earlier stage.
• Ontogeny can be shortened in evolution.
• Terminal stages may be deleted causing adults of
  descendants to resemble youthful ancestors.
• Paedomorphosis
• Retention of ancestral juvenile characters by
  descendant adults.

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Developmental Modularity and Evolvability

• Heterotopy a change in the physical location of
  a developmental process in an organisms body.
• Process must be compartmentalized into
  semi-autonomous modules to be expressed in new
  location
• Ex Location of toepad development in geckos.

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Vestigial Organs

• Vestigial organs remnants of structures that
  served important functions in an ancestor.
• Remnants of pelvis and leg bones in snakes
• Appendix in humans

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Molecular Homologies

• Similarities can be found at the molecular level,
  too.
• The genetic code is universal - it is likely that
  all organisms descended from a common ancestor.
• Different organisms share genes that have been
  inherited from a common ancestor.
• Often, these genes have different functions, like
  the mammalian forelimbs.

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Homologies the Tree of Life

• Darwins evolutionary tree of life can explain
  homologies.
• The genetic code is shared by all species because
  it goes back deep into the ancestral past.
• More recent homologies are shared by only smaller
  branches of the tree.

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Homologies the Tree of Life

• Homologies result in a nested pattern.
• All life shares the deepest layer.
• Each smaller group adds homologies to those they
  share with larger groups.

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Speciation

• Speciation refers to the formation of new
  species.
• Defining a species is difficult
• Descent from common ancestral population.
• Ability to interbreed.
• Maintenance of genotypic phenotypic cohesion.
• Reproductive barriers prevent species from
  interbreeding.
• Where do they come from?

54
Allopatric Speciation

• Allopatric (another land) populations occupy
  separate geographic areas.
• Separated geographically, but able to interbreed
  if brought together.
• Over time, reproductive barriers may evolve so
  that they could not interbreed.
• Allopatric speciation

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Allopatric Speciation

• The geographical separation can arise in two
  ways
• Vicariant speciation is initiated when climatic
  or geological changes fragment a species
  habitat, forming impenetrable barriers.
• Founder events occur when a small number of
  individuals disperse to a distant place where no
  other members of their species exist.

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Hybrids

• Much can be learned by studying what happens when
  previously isolated populations come into contact
  again.
• Hybrids are offspring of members of two closely
  related species.

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Hybrids

• Species eventually become different enough that
  they cant produce hybrids.
• Premating barriers prevent mating from occurring
  in the first place.
• Postmating barriers impair growth, survival, or
  reproduction of the offspring.

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Sympatric Speciation

• Sympatric (same land) speciation occurs when
  speciation occurs in one geographic area a lake
  for example.
• Individuals within the species become specialized
  on a food type, shelter, part of the lake etc.
• Eventually reproductive barriers evolve.

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Parapatric Speciation

• Parapatric Speciation geographically
  intermediate between allopatric and sympatric
  speciation.
• Two species are parapatric if their geographic
  ranges are primarily allopatric but make contact
  along a borderline that neither species
  successfully crosses.

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Adaptive Radiation

• Adaptive radiation the production of
  ecologically diverse species from a common
  ancestral stock.
• Common in lakes islands sources of new
  evolutionary opportunities.

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Adaptive Radiation

• Archipelagoes increase opportunities for both
  founder events and ecological diversification.
• Entire archipelago isolated from the continent.
• Each island is geographically isolated from the
  others.
• Ex Galápagos Islands

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Gradualism

• Darwins theory of gradualism proposes that small
  differences accumulate over time producing the
  larger changes we see over geologic time.
• Certainly, this process is always at work, but
  probably does not account for all changes.

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Punctuated Equilibrium

• Punctuated equilibrium states that phenotypic
  evolution is concentrated in relatively brief
  events of branching speciation followed by
  periods of stasis.

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Populations Evolve

• Variation exists within any population.
• When natural selection acts to favor one trait
  over another that trait will increase in the
  population.
• The population has evolved, not any one
  individual.

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The Modern Synthesis

• Population Genetics the study of how
  populations change over time.
• Dependent on both Darwins theory of natural
  selection and Mendels laws of inheritance.
• All heritable traits have a genetic basis, some
  are controlled by multiple genes not as simple
  as in Mendels studies.

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The Modern Synthesis

• The modern synthesis is a comprehensive theory of
  evolution that brings in ideas from many fields.
• R. A. Fisher (statistician)
• J. B. S. Haldane (biologist)
• Theodosius Dobzhansky (geneticist)
• Sewall Wright (geneticist)
• Ernst Mayr (biogeographer)
• George Gaylord Simpson (paleontologist)
• G. Ledyard Stebbins (botanist)

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Populations

• Population a localized, interbreeding group of
  individuals of a particular species.
• Separate populations of a species may be isolated
  from each other.

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Populations

• Sometimes the populations overlap, but little
  interbreeding occurs.

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Microevolution

• Microevolution evolutionary changes in the
  frequency of alleles in a population.
• Polymorphism occurrence of different allelic
  forms of a gene in a population.
• If there is only one allele for a gene in the
  population every individual is homozygous for
  the trait it is fixed in the population.
• All alleles of all genes possessed by all members
  of a population form a gene pool.

70
Microevolution

• Population geneticists measure the relative
  frequencies of alleles in the population.
• Allelic frequency

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Genetic Equilibrium

• According to Hardy-Weinberg equilibrium, the
  hereditary process alone does not produce
  evolutionary change.
• Allelic frequency will remain constant generation
  to generation unless disturbed by mutation,
  natural selection, migration, nonrandom mating,
  or genetic drift.
• Sources of microevolutionary change.

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Frequency of Alleles

• Each allele has a frequency (proportion) in the
  population.
• Example population of 500 wildflowers.
• CRCR red CRCW pink CWCW white
• 320 red, 160 pink, 20 white
• Frequency of CR
• (320 x 2) 160 / 1000 800/1000 .8 80

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Frequency of Alleles

• p is the frequency of the most common allele (CR
  in this case).
• p 0.8 or 80
• q is the frequency of the less common allele (CW
  in this case).
• p q 1
• q 1- p 1 0.8 0.2 or 20

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Hardy-Weinberg Theorem

• Populations that are not evolving are said to be
  in Hardy-Weinberg equilibrium.
• As long as Mendels laws are at work, the
  frequency of alleles will remain unchanged.

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Hardy-Weinberg Theorem

• The Hardy-Weinberg theorem assumes random mating.
• Generation after generation allele frequencies
  are the same.

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Hardy-Weinberg Theorem

• At a locus with two alleles, the three genotypes
  will appear in the following proportions
• (p q) x (p q) p2 2pq q2 1

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Hardy-Weinberg Theorem

• Conditions
• Very large population
• No gene flow into or out of the population
• No mutations
• Random mating
• No natural selection
• Departure from these conditions results in
  evolution.

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Practice with Hardy Weinberg

• Hardy Weinberg studied the frequencies of
  alleles in populations.
• Frequency the proportion of individuals in a
  category in relation to the total number of
  individuals. 100 cats, 84 black, 16 white
  frequency of black 84/100 0.84, white 0.16.
• Two alleles p is common, q is less common.
• pq 1

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Practice with Hardy Weinberg

• (p q)2 p2 2pq q2

Individuals homozygous for allele B
Individuals heterozygous for alleles B b
Individuals homozygous for allele b
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Practice with Hardy Weinberg

• Used to calculate allele frequencies (p q) in a
  simple way.
• 100 cats, 16 white (bb) so q2 0.16
• q square root of 0.16 0.40.
• Since p q 1 p 1 q 0.60.
• p2 0.36 so 36 homozygous dominant (BB)
• 2pq 0.48 48 heterozygous (Bb)

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Where Does Variation Come From?

• Natural selection acts on the variation that is
  already present in the population.
• But, where did that variation come from?

82
Where Does Variation Come From?

• Two processes provide the variation in gene
  pools.
• Mutation
• Sexual recombination

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Mutation

• New genes or alleles only result by mutations.
• Mutations are changes in the nucleotide sequence
  of DNA.

84
Point Mutations

• Point mutation a change in a single base pair.
• Often harmless
• Much of the DNA does not code for protein
  products.
• Genetic code is redundant.
• CGU, CGA, CGC, CGG all code for argenine.
• Occasionally significant
• Sickle cell disease.

85
Mutations

• Beneficial mutations of any kind are very rare.
• Mutations that alter gene number or sequence are
  almost always harmful.

86
Gene Duplication

• Gene duplication occasionally provides an
  expanded genome with new loci that may take on
  new functions as selection continues.
• New genes can also appear when non-coding introns
  get shuffled into the coding portion of the
  genome.

87
Sexual Recombination

• Sexual recombination is a much more common way of
  producing variation in populations.
• Reshuffling of allele combinations already
  present in the population is how variation is
  maintained in populations.
• Sexual reproduction rearranges alleles into fresh
  combinations every generation.

88
Natural Selection

• When natural selection is occurring, some
  individuals are having better reproductive
  success than others.
• Alleles are being passed to the next generation
  in frequencies that are different from the
  current generation.
• Hardy-Weinberg equilibrium is upset.

89
Genetic Drift

• The smaller the sample, the greater the chance of
  deviation from expected results.
• These random deviations from expected frequencies
  are called genetic drift.
• Allele frequencies are more likely to deviate
  from the expected in small populations.

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Genetic Drift

• Which allele was lost is due to random chance.
• Over time, drift tends to reduce genetic
  variation through random loss of alleles.

91
The Bottleneck Effect

• Sometimes a catastrophic event can severely
  reduce the size of a population.
• The random assortment of survivors may have
  drastically different allele frequencies.
• Bottleneck effect

92
The Bottleneck Effect

• The actions of people sometimes cause bottlenecks
  in other species.
• N. California elephant seal population reduced to
  20-100 individuals in the 1890s.
• Current population gt 30,000.
• Variation drastically reduced 24 genes with 1
  allele.

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93
The Founder Effect

• Founder effect When a small group of
  individuals becomes separated from the population
  and form a new population, the allele frequencies
  in their gene pool may be different than the
  original population.

94
Gene Flow

• The population can gain or lose new alleles
  through gene flow.
• When individuals move into or out of a
  population, they may carry the only copy of
  certain alleles in the gene pool with them.
• Gene flow usually reduces differences between
  populations.

95
Natural Selection Adaptation

• Natural selection is the only one of these ways
  of altering the gene pool that results in
  adaptation.
• Selection depends on variation.

96
Genetic Variation

• Variation in a population is always present.
• Heritable variation is the raw material of
  natural selection.

97
Genetic Variation

• Not all genetic variation is heritable.
• Environmental influences sometimes effect
  phenotype.

98
Polymorphism

• Different versions of discrete characters are
  called morphs.
• When a population has two or more morphs that are
  common in the population, it is called
  polymorphic.
• This is phenotypic polymorphism

99
Protein Polymorphism

• Different allelic forms of a gene code for
  slightly different proteins protein
  polymorphism.
• If the difference affects the proteins net
  electric charge, the different forms can be
  separated using protein electrophoresis.

100
Quantitative Variation

• Quantitative traits are those that show
  continuous variation.
• Influenced by many genes.
• Height in humans, tail length in mice
• When trait values for a population are graphed,
  they follow a bell shaped curve.

101
Modes of Selection

• Stabilizing removes the extremes.
• Directional variants at one of the extremes are
  favored.
• Disruptive variants at both extremes are
  favored.

102
Evolutionary Fitness

• Fitness the contribution an individual makes to
  the gene pool of the next generation.
• Relative fitness the contribution of one
  genotype relative to the contribution of other
  genotypes at the same locus.
• Natural selection acts on phenotypes.

103
Preserving Variation

• Some variation is hidden from the natural
  selection process in the form of recessive
  alleles in heterozygotes.
• Less favorable recessive alleles can be
  maintained in the population because they do not
  harm heterozygous individuals.

104
Sexual Selection

• Sexual selection natural selection for mating
  success.
• May result in sexual dimorphism differences
  between the sexes.
• Secondary sexual characteristics not directly
  involved in reproduction.

105
Intrasexual Selection

• Intrasexual selection selection within the same
  sex results when individuals of one sex are
  competing with each other for members of the
  other sex.
• Features that make the male a better fighter or
  more intimidating to other males would be favored.

106
Intersexual Selection

• Intersexual selection mate choice individuals
  of one sex are choosy in selecting a mate.
• Features that make an individual more attractive
  to the opposite sex would be favored.

107
Intersexual Selection

• Showiness that results from mate choice can be
  risky.
• Flashy tails of guppies make them more visible to
  predators.
• Benefits of finding a mate outweigh potential
  costs.
• Showiness may reflect overall health.

108
Macroevolution

• Macroevolution refers to grand scale events in
  evolution.
• Evolution of new structures
• Major trends in the fossil record

109
Goulds Tiers of Time

• Stephen Jay Gould recognized three tiers of time
  for evolutionary processes
• Tens to thousands of years population genetic
  processes.
• Millions of years speciation and extinction can
  be measured and compared among different groups
  of organisms.
• Tens to hundreds of millions of years marked by
  episodic mass extinctions.

110
Speciation and Extinction Through Geological Time

• A species has two possible fates
• Become extinct or
• Give rise to new species.
• Speciation and extinction rates vary among
  species.
• Lineages with high speciation and low extinction
  produce the greatest diversity.

111
Mass Extinctions

• Mass extinctions are episodic events where many
  species go extinct at the same time.
• Permian extinction 225 MYA half the families
  of shallow-water marine invertebrates and 90 of
  the marine invertebrate species went extinct over
  a few million years.
• Cretaceous extinction 65 MYA marks the end of
  the dinosaurs as well as many other species.

112
Mass Extinctions

• Many possible explanations for mass extinctions
  have been suggested.
• Alvarez hypothesis bombardment of the earth by
  asteroids would send debris into the atmosphere,
  altering climate.
• Search for evidence
• Craters
• Atypical iridium concentrations

113
Mass Extinctions

• Catastrophic species selection would result from
  selection by these events.
• Mammals were able to use resources due to
  dinosaur extinction.

114
Endurance of Darwins Theory

• The beauty of Darwins theory is that it explains
  so many different kinds of observations
  anatomical and molecular homologies that match
  patterns in space (biogeography) and time (fossil
  record).

"Nothing in biology makes sense except in the
light of evolution." Theodosius Dobzhansky,
Geneticist