Download Evolution Notes

Today’s Plan: 2/25/11
 Bellwork: Go over test/fly counts (30
mins)
 Amino Acid Sequence and Evolution
Lab (30 mins)
 Begin Natural Selection Notes (the
rest of class)
 Pack/Wrap-up (last few mins of class)
Today’s Plan: 2/26/10
 Bellwork: Finish Flies/Compile Class
Data (30 mins)
 Sexual Selection Video
 Pack/Wrap-up (last few mins of class)
Today’s Plan: 3/1/10
 Bellwork: Go over lab/Do PTC (15
mins)
 AP Lab 8: Population Genetics and
Evolution-Part B Genetic Drift (20
mins)
 Finish video
 Continue Notes-if time
 Pack/Wrap-up (last few mins of class)
Today’s Plan: 3/2/10
 Bellwork: Settle in/Grab cards (5
mins)
 Finish Lab (30 mins)
 Continue notes (25 mins)
 Pack/Wrap-up (last few mins of class)
Today’s Plan: 3/3/10
 Finish Notes (30 mins)
 Restriction Mapping Exercise (the rest
of class)
 Pack/Wrap-up (last few mins of class)
Today’s Plan: 3/4/10
 Bellwork: Finish Restriction Mapping
(20 mins)
 Finish Nat. Sel Notes (20 mins)
 HB fun week (the rest of class)
Today’s Plan: 3/5/10
 HB Stations-the entire period!
Before Natural Selection

Recall that Darwin wasn’t the 1st to think about how species have
changed over time
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Aristotle’s Scala Naturae grouped species with similar “affinities”
together
Linnaeus came up with Binomial Nomenclature and did much
classifying based on physical similarity
Cuvier noted that fossils of species differed significantly from more
modern forms (proposed the idea of Catastrophism-that changes
happened b/c of catastrophic events, and not gradually)
Lamarck suggested that use/disuse and will could change an
organism’s body to fit the environment (he thought that acquired traits
were heritable)
Malthus also discussed population limits
Darwin bred pigeons for various traits (artificial selection)
Recall that besides thinking about species change, others before
Darwin worked with how the planet changed
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Hutton proposed that geologic features were the result of gradual
changes that are still occurring today
Lyell took this a step further and proposed his principle of
Uniformitarianism-mechanisms of change are constant over time
Figure 24-1
Natural Selection
 Aka “Descent with Modification” was Darwin’s
proposal for how species change over time and was
the result of careful ponderance over his Galapagos
Island collections
 Darwin’s main focus was on adaptations that allowed
species to survive better in their environments-finches
had beaks adapted to their food source
 Recall that while Darwin came up with the idea first,
Alfred Russel Wallace also had the same ideal later,
with no knowledge of Darwin’s work
 The term Natural Selection was coined by Darwin’s
friend, T.H. Huxley, who was called “Darwin’s bulldog”
because he staunchly defended Darwin’s hypothesis
Darwin’s Observations and
Inferences
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Observations:
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Inferences (Summary of Natural Selection’s Mechanism):
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Members of a population vary greatly in their traits
Traits are inherited from parents to offspring
All species are capable of producing more offspring than their
environment can support
Because of lack of resources, many offspring don’t survive
Individuals whose inherited traits give them a higher
probability of surviving and reproducing in an environment
tend to leave more offspring (have greater reproductive
success)
This inequality means that favorable traits accumulate in
populations over multiple generations
Remember:
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Populations evolve, individuals don’t
Traits influenced by natural selection must be heritable
Environments are moving targets, so there’s no “perfect” and
what’s good in one population isn’t necessarily good in another
Current Directly Observable
Evidence for Natural Selection
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Predation and Coloration in Guppies
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Drug-resistant HIV and other “superbugs”
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Pools of guppies w/high predation produce more drab colored males
There are numerous examples of these “natural experiments” done by
scientists
It’s natural for some viruses or bacteria to be resistant, but when you
treat, what’s all that’s left to reproduce?
The Fossil Record
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We can see trends in the evolution of species
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Similar patterns of fetal development
Homology (forelimb picture)
Vestigial structures
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Looking at what we think happened to the geographic features of the
planet to explain distribution of species (ex: how Pangea’s split allowed
us to predict where we’d find certain types of fossils)
Anatomical Features
Biogeography
Molecular Similarity

Studies of DNA sequence and amino acid sequence can be used to
construct “molecular clocks” that give us clues to which organisms
diverged from one another, and tells us relatively how long ago the
divergance occurred
Figure 24-11
1. Large population of
2. Drug therapy begins killing
3. The mutant cells proliferate,
4. A second round of
M. tuberculosis bacteria in
patient’s lungs makes him sick.
most M. tuberculosis. Patient
seems cured and drug therapy
is ended. However, a few of the
original bacteria had a point
mutation that made them
resistant to the drug treatment.
resulting in another major
infection of the lungs. The
patient becomes sick again.
drug therapy begins but
is ineffective on the drugresistant bacteria. The
patient dies.
Figure 24-3
Figure 24-9
Figure 24-8
Figure 24-5
Figure 24-7
Figure 27-7
Tree thinking vs. Convergent
evolution
 In many cases, evolutionary trees are
created in order to show how species
evolved from common ancestors
 Sometimes, this happens b/c of adaptive
radiation-when organisms evolve in a variety of
directions in order to exploit different aspects of
the environment
 Occasionally, organisms resemble each
other, not because they’re related, but
because some characteristics are
advantageous regardless of their ancestry
 Ex: sugar gliders in Australia look like flying
squirrels
Figure 27-11
Figure 24-15b
Darwinian evolution produces a tree of life.
Common ancestor of
all species living today
The branches on the tree
represent populations
through time. All of the
species have evolved from
a common ancestor. None
is higher than any other
Sexual Selection
 This is a variation of natural selection where some
traits persist, not because they’re advantageous, but
because they’re attractive
 In some cases, the traits that evolve are
disadvantageous, but continue to persist
 Intersexual Selection is based on the “female choice”
model-the opposite sex chooses a mate
 Intrasexual Selection is based on competition within
the sex for access to mates or resources that will
attract mates
 Causes sexual dimorphism (variation between sexes)
Figure 25-15
Beetle
Scarlet tanager
Lion
Females
Males
During the breeding season, males of the Male scarlet tanagers use their bright
beetle Dynastes granti use their elongated coloration in territorial and courtship
horns to fight over females.
displays.
Male lions are larger than females lions and
have an elaborate ruff of fur called a mane.
Figure 25-14
Males compete to mate with females.
Variation in reproductive success is high in males.
Variation in reproductive success is relatively low in females.
The survival of the fittest. . .
 Remember, fitness is relative, and
“struggle” isn’t always direct conflict.
 Depending on which traits are favored,
there are 3 ways in which natural selection
can influence phenotypic variation
 Directional selection-one extreme phenotype is
favored
 Disruptive selection-both extreme phenotypes
are favored
 Stabilizing selection-average is favored
Figure 25-3
Directional selection changes the average value of
a trait.
Normal distribution
For example, directional selection caused average body
size to increase in a cliff swallow population.
Original population
(N = 2880)
Before selection
Survivors
(N = 1027)
Low
fitness
During selection
After selection
Change in
average
value
High
fitness
Change in
average
value
Figure 25-4
Stabilizing selection reduces the amount of variation
in a trait.
For example, very small and very large babies are the
most likely to die, leaving a narrower distribution of birth
weights.
Normal distribution
Mortality
Before selection
Low High fitness Low
fitness
fitness
During selection
After selection
Reduction
in variation
Heavy
mortality
on extremes
Figure 25-5
Disruptive selection increases the amount of variation
in a trait.
For example, only juvenile black-bellied seedcrackers that
had very long or very short beaks survived long enough to
breed.
Normal distribution
Before selection
Only the
extremes
survived
High
fitness
Low fitness
High
fitness
During selection
Increase in
variation
After selection
Only the
extremes
survived
Evolution of Populations
 This is fueled by genetic variation
 For individuals, can be quantified using average
heterozygosity (average % of genes for which an
individual is heterozygous)
 For populations, you can directly compare individual
karyotypes or gene sequences from each population
 Sometimes, the difference is dramatic, and sometimes
the difference is a cline (gradual difference)
 This often exists b/c of geographic variation (isolation)
 Genetic Variation occurs for 2 reasons
 Sexual Reproduction
 Mutation is the ultimate source for most new genetic
variations. Often these mutations are neutral, but
occasionaly, you get an adaptive mutation. The rates
at which mutation occurs varies between species.
Hardy-Weinberg
 Useful for testing whether or not a
population is evolving
 This is a mathematical model:
 p2+2pq+q2=1
 p=frequency of the dominant allele
 q=frequency of the recessive allele
 When a population is in Hardy-Weinberg
equilibrium, the equation works, but when
populations are evolving, it is an
inequation.
Figure 24-10
Figure 25-1-1
A NUMERICAL EXAMPLE OF THE HARDY-WEINBERG PRINCIPLE
Allele frequencies in parental generation: Allele A1
= p = 0.7
1. Suppose allele frequencies
Allele A2
= q = 0.3
in the parental generation were
0.7 and 0.3.
Gene pool (gametes from parent generation)
2. 70% of gametes in the gene
pool carry allele A1, and 30%
carry allele A2.
A1
A1
0.7  0.7 = 0.49
p  p = p2
A1
A2
0.7  0.3 = 0.21
q  p = pq
A2
A1
0.3  0.7 = 0.21
q  p = pq
0.21 + 0.21 = 0.42
A2
A2
0.3  0.3 = 0.09
q  q = q2
3. Pick two gametes at random
from the gene pool to form
offspring. You have a 70%
chance of picking allele A1 and a
30% chance of picking allele A2.
Figure 25-1-2
A NUMERICAL EXAMPLE OF THE HARDY-WEINBERG PRINCIPLE
Frequency of
A1A1 genotype is
p2 = 0.49
Frequency of
A1A2 genotype is
2pq = 0.42
Frequency of
A2A2 genotype is
q2 = 0.49
4. Three genotypes are possible.
Calculate the frequencies of these
three combinations of alleles.
5. When the offspring breed,
49% of offspring have
the A1 A1 genotype. All
will contribute A1 alleles
to the new gene pool.
42% of offspring have the A1 A2
Genotype. Half of their gametes
will carry the A1 allele and the
other half will carry the A2 allele.
9% of offspring have
the A2 A2 genotype. All
will contribute A2 alleles
to the new gene pool.
imagine their gametes entering
a gene pool. Calculate the
frequencies of the two alleles
in this gene pool.
6. The frequencies of A1 and A2
Allele frequencies in
offspring gene pool
1
p = 0.49 + 2 (0.42) = 0.7
p = frequency of allele A1
q = 12 (0.42) + 0.09 = 0.3
q = frequency of allele A2
have not changed from parental
to offspring generation.
Evolution has not occurred.
Genotype frequencies will be given by p2 : 2 p q : q2 as long as all Hardy-Weinberg assumptions are met.
Conditions for Hardy-Weinberg
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No mutation
Random Mating
No natural selection
Large population size
No gene flow
Rarely do all of these conditions exist
at any given moment, but over time,
populations tend to be in equilibrium
Altering Gene Frequencies
 Genetic Drift-caused by small population size or
random changes that make predicting gene frequency
difficult. 2 examples:
 The founder effect-a small number of individuals are
isolated from the larger group and have to
reestablish a gene pool
 The bottleneck effect-catastrophic incidents drop
population size quickly and dramatically
 In either case, genetic variation is lost, and harmful
alleles can persist
 Gene Flow-occurs when genes transfer in and out of
populations. Usually, this is negligible unless
something causes any of the following factors to
change dramatically:
 Immigration
 Emigration
Figure 25-6
Figure 25-8
Lupines colonize sites and form populations.
Gene flow reduces genetic differences among populations.
Year 1: Seed establishes new population
Year 2: Gene flow between source population and new population
New population
Source population
Seed
A1A1
A1A1
A1A1
A1A1
A1A2
New population
Source population
Gene
flow
A1A2
A1A1
A1A1
A1A2
A1A1
A1A2
A1A1
A1A1
A1A2
A1A2
Frequency of A1 = 0.90
Frequency of A1 = 0.50
Frequency of A1 = 0.83
Frequency of A1 = 0.67
Frequency of A2 = 0.10
Frequency of A2 = 0.50
Frequency of A2 = 0.17
Frequency of A2 = 0.33
Initially, allele frequencies
are very different
Gene flow causes allele
frequencies to become
more similar
Preserving Genetic Variation
 Diploidy-Since organisms get 2 copies of
each gene, recessive alleles can be
preserved
 Balancing Selection-occurs when natural
selection maintains 2 forms of a trait in a
population
 The heterozygote advantage-sickle cell disease
and malaria symptom resistance
 Frequency-Dependent selection-as a phenotype
becomes more common, it loses its advantage
 Neutral Variation-occurs when mutation has
little to no effect on phenotype or on
reproductive success
Why isn’t there a “perfect”
organism
 Selection can only act on existing variations
(and each intermediate step between
phenotypes must be adaptive)
 You can’t scrap ancestral anatomy to build
something new (see above statement)
 Adaptations are often compromises
(multifunctionality means you have to
choose a primary function. Ex: seals don’t
have legs b/c they also swim)
 Chance, natural selection, and the
environment have to interact
Types of evolution
 Microevolution-evolution of allele
frequencies within gene pools
 Macroevolution-patterns of evolution
over long time spans (like the
emergence of new species)
The Biological Species Concept
 This is the classic definition of the
term “species” put forth by Ernst
Mayr
 A species is a group of populations
whose members interbreed in nature
to produce fertile offspring
 Species are held together by
proximity and interbreeding
Making new species
 Requires Reproductive isolation-barriers
that prevent the production of viable
offspring (remember that hybrids can exist,
but are sterile: ligers, mules, etc)
 Prezygotic barriers-block fertilization
 Blocking mating
 Blocking the successful completion of mating
 Preventing successful fertilization
 Postzygotic barriers-prevent a hybrid from
mating successfully
Types of Prezygotic Mechanisms
 Habitat Isolation-2 species occupy different
habitats
 Temporal Isolation-species breed at
different times
 Behavioral Isolation-courtship rituals differ
 Mechanical Isolation-differences in
shape/form prevent mating
 Gametic Isolation-the gametes may not be
able to fuse
Types of postzygotic Mechanisms
 Reduced Hybrid viability-parental
genes prevent the hybrid’s survival
 Reduced Hybrid Fertility-sterility due
to inability to produce normal
gametes
 Hybrid Breakdown-Some hybrids can
mate with one another, but their
offspring are not viable
Limitations of Biological Species
 It’s hard to evaluate the reproductive isolation of
fossils, nor does it address species that reproduce
asexually
 Other species definitions
 Morphological species concept-characterizes species
by body shape and structure (can be applied to
sexual and asexual reproducers, however this relies
on subjective criteria)
 Ecological species concept-characterizes a species
based on its ecological niche (also can be applied to
sexual and asexual reproducers, and emphasizes the
role of disruptive selection in species definition)
 Phylogenetic species concept-a species is defined by
the smallest group of individuals that share a
common ancestor (difficult to deterime the degree of
difference required to separate one species from
another)
Allopatric Speciation
 “other country” speciation-occurs when
species are geographically isolated
 Populations become divided and evolve
differently because of different
environments, genetic drift, and different
mutations
 Remember that they’re not different
species until they’re reproductively isolated.
If the populations are put back together
and can still mate, they’re not different
species
Figure 26-5
DISPERSAL AND COLONIZATION CAN ISOLATE POPULATIONS.
Island
Continent
1. Start with one continuous
2. Island population begins
3. Finish with two populations
population. Then, colonists
float to an island on a raft.
to diverge due to drift and
selection.
isolated from one another.
VICARIANCE CAN ISOLATE POPULATIONS.
River
1. Start with one continuous
2. Isolated populations begin
3. Finish with two populations
population. Then a chance
event occurs that changes
the landscape (river changes
course.)
to diverge due to drift and
selection.
isolated from one another.
Sympatric Speciation
 “same country” speciation-occurs when organisms are
in the same area but speciate
 Can occur via several mechanisms:
 Polyploidy-having an extra set of chromosomes
 Autopolyploid-more than 2 sets of chromosomes from a
single species (failure of cell division)
 Allopolyploid-caused by an extra set of chromosomes
via hybridization of 2 species (fertile when mating with
one another only)
 Habitat Differentiation-when a subpopulation exploits
a resource that the rest of the population doesn’t
 Sexual Selection-when different groups of females
prefer different groups of males
Figure 26-7
Soapberry bugs use their beaks to reach seeds inside fruits.
Feeding on
the fruit of
a nonnative
species
Feeding
on the
fruit of
a native
species
Nonnative fruits are much smaller than native fruits.
Nonnative plant
(small fruit)
Native plant
(large fruit)
Evidence for disruptive selection on beak length
Short-beaked
population
growing on
nonnative
plants
Long-beaked population
growing on native plants
Figure 26-8
Diploid parent
(Two copies of
each chromosome)
Tetraploid parent
(Four copies of
each chromosome)
Meiosis
Haploid gametes
Diploid gametes
(Two copies of
(One copy of
each chromosome) each chromosome)
Mating
Triploid zygote
(Three copies of
each chromosome)
Meiosis
Gametes
The gametes of a triploid individual rarely contain the same number of
each type of chromosome. When gametes combine, offspring almost
always have an uneven (dysfunctional) number of chromosomes.
Hybrid Zones
 When allopatric species come back into
contact with one another, you get a hybrid
zone
 There are several possibilities for what can
happen in a hybrid zone
 Reinforcement-occurs when hybrids are less fit
than the parent species
 Fusion-occurs when reproductive barriers are
weak and the species become increasingly alike
 Stability-occurs when the hybrids persist
Figure 26-11
Hybrids have intermediate characteristics.
Hybrids inherit species-specific mtDNA sequences from their mothers.
Townsend’s warbler
All individuals have
Townsend’s mtDNA
Present range
of Townsend’s
warblers
(in red)
Townsend’s-hermit
hybrid
Pacific Ocean
Individuals that look like
Townsend’s warblers but
have hermit mtDNA
Some individuals
have Townsend’s
mtDNA, others
have hermit
mtDNA
Present hybrid
zones (where
two ranges
meet)
Hermit warbler
Present range
of hermit
warblers
(in orange)
All individuals have
hermit mtDNA
Speciation Rates
 Darwin originally believed that gradualism
existed (species change at a slow, steady
rate over time)
 From the fossil record, we now know that
punctuated equilibrium exists (periods of
equilibrium followed by periods of natural
selection)
 This can happen very rapidly, and as little
as 1 gene can make a species
reproductively isolated
Geologic Time
 This is a time scale that uses the
fossil record to trace the major
events in the planet’s history
 Dates are determined by dating
fossils
 Relative Dating-accomplished via the law
of superposition
 Absolute Dating-accomplished via
radiometric dating
Figure 27-5
HOW FOSSILIZATION OCCURS
Earth’s History
 Earth is believed to have existed for 4.6
billion years
 Life on earth is believed to have originated
3.5 billion years ago.
 The first life forms were probably prokaryotes
 There have been 5 mass extinctions over
the history of the planet, and in each, the
dominant group of organisms was replaced
by another group
Figure 27-8a
Figure 27-8b
Figure 27-8c
Figure 27-8d
Figure 27-5
HOW FOSSILIZATION OCCURS
Major events in Earth’s History:
 The earth cools
 1st life forms
 Accumulation of
atmospheric
oxygen
 1st eukaryotes
 Multicellular
organisms
 Animals evolved
 Plants and fungi
colonized land
 Land became
colonized by other
organisms
Where would life come from?
 Recall that Miller and Urey tested Oparin’s primordial
soup hypothesis and were able to create biochemicals
 Lab experiments since then have been able to form
polymers in conditions similar to early earth
 RNA was probably the 1st genetic material
 These have been shown to be produced abiotically in
the lab
 Recall that Ribozymes exist as well.
 Protobionts can self-assemble
 These are aggregates of abiotically produced
molecules that form “membranes” and often can
sustain chemical reactions (like a metabolism)
What about Eukaryotic cells?
 One current hypothesis, the
endosymbiant hypothesis tries to
explain this
 Mitochondria have their own DNA,
resemble bacteria, and replicate
themselves for cell division
 This suggests that once the 1st primitive
cells evolved, they “swallowed” other
cells. It is believed that they could have
become dependent on one another to
carry out parts of their metabolism