Today’s Plan: 8/27/18

 Sit at a seat that has paperwork and

begin filling out the notecard with the
following:
 Your preferred first name and last name
 FRONT if you have to sit in the front of
the room
 Your book number
 Go over syllabus, books (30 mins)
 Begin Mechanism of Natural Selection
notes, FRQ prep
Today’s Plan:12/2/19
 Bellwork: Go over Test FRQ (10 mins)
 Go over restriction mapping and
practice (20 mins)
 Natural Selection Practice FRQ-
INDIVIDUALLY DONE!
 If time-start natural selection notes
(the rest of class)
Today’s Plan: 12/3/19
 Natural Selection notes (20 mins)
 Hardy-Weinberg POGIL (40 mins)
 PTC Testing (Natural Selection lab
Part A)
Today’s Plan: 12/4/19
 Bellwork: HW Lab Part A with sample
calculations and HW discussion (30
mins)
 Data-gathering (the rest of class)
Today’s Plan: 12/5/19
 Bellwork: FRQ Progress Check,
question 1 (30 mins)
 Finish H-W lab (45 mins)
 Continue notes (the rest of class)
Today’s Plan: 12/6/19
 BW: Selection and Speciation POGIL
Model 1 (15 mins)
 Graphing practice (15 mins)
 Model 2 & 3 (the rest of class)
 If time-start speciation notes
Today’s Plan: 12/9/19
 Bellwork: Speciation POGIL Model 2
(20 mins)
 Speciation notes (20 mins)
 Speciation practice and POGIL Model
3 (the rest of class)
Today’s Plan: 12/10/19
 Sexual Selection Video and discussion
(60 mins)
 Wrap-up notes (10 mins)
 Check your Selection and Speciation
POGIL, Model 3 if you haven’t already
Today’s Plan: 12/13/19
 Bellwork: Read the background and
questions for the practice FRQ (10
mins)-Take notes as you read!
 As a table-create a poster with visuals to
answer the questions (30 mins)
 Gallery walk with rubric and +1 (10
mins)
 Revisions based on feedback (10 mins)
 Review Origin of Life info so far (the rest
of class)
Today’s Plan: 12/16/19
 Bellwork: (20 mins)Take notes on the online
tutorial at
https://evolution.berkeley.edu/evolibrary/articl
e/0_0_0/origsoflife_01
 Read the background info for your “side” of the
debate on origin of life (10 mins)
 Construct a poster describing your “side” (15
mins)
 Gallery walk within “sides” to add suggestions
(15 mins)
 Read/take notes on debate info (the rest of
class)
Today’s Plan: 12/17/19
 Bellwork: Gallery walk the other
“side” posters, adding +1
counterarguments (20 mins)
 Geologic Time Activity (40 mins)
 Geologic time notes (the rest of class)
Today’s Plan: 12/18/19
 Bellwork: Finish notes on Geologic
time (15 mins)
 Extinction activity (the rest of class)
Before Natural Selection
 Recall that Darwin wasn’t the 1st to think about how species have
changed over time
 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
 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
 Observations:
 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
 Inferences (Summary of Natural Selection’s Mechanism):
 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:
 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
 Predation and Coloration in Guppies
 Pools of guppies w/high predation produce more drab colored males
 There are numerous examples of these “natural experiments” done by
scientists
 Drug-resistant HIV and other “superbugs”
 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
 We can see trends in the evolution of species
 Anatomical Features
 Similar patterns of fetal development
 Homology (forelimb picture)
 Vestigial structures
 Biogeography
 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)
 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
M. tuberculosis bacteria in
patient’s lungs makes him sick.
2. Drug therapy begins killing
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.
3. The mutant cells proliferate,
resulting in another major
infection of the lungs. The
patient becomes sick again.
4. A second round of
drug therapy begins but
is ineffective on the drug-
resistant bacteria. The
patient dies.
Figure 24-3
Figure 24-9
Figure 24-8
Figure 24-5
Figure 24-7
Figure 27-7
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
 Works with p+q=1
 When a population is in Hardy-Weinberg
equilibrium, the frequencies of the
genotypes and alleles doesn’t change. If it
changes each generation, then the
population is evolving.
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
in the parental generation were
= q = 0.3
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 A1 A2 A2 A1
3. Pick two gametes at random
A2 A2
from the gene pool to form
0.7  0.7 = 0.49 0.7  0.3 = 0.21 0.3  0.7 = 0.21 0.3  0.3 = 0.09 offspring. You have a 70%
q  p = pq q  p = pq chance of picking allele A1 and a
p  p = p2 q  q = q2
30% chance of picking allele A2.
0.21 + 0.21 = 0.42
Figure 25-1-2

A NUMERICAL EXAMPLE OF THE HARDY-WEINBERG PRINCIPLE

Frequency of Frequency of Frequency of 4. Three genotypes are possible.

A1A1 genotype is A1A2 genotype is A2A2 genotype is Calculate the frequencies of these
p2 = 0.49 2pq = 0.42 q2 = 0.49 three combinations of alleles.

5. When the offspring breed,

49% of offspring have 42% of offspring have the A1 A2 9% of offspring have imagine their gametes entering
the A1 A1 genotype. All Genotype. Half of their gametes the A2 A2 genotype. All a gene pool. Calculate the
will contribute A1 alleles will carry the A1 allele and the will contribute A2 alleles frequencies of the two alleles
to the new gene pool. other half will carry the A2 allele. to the new gene pool. in this gene pool.

6. The frequencies of A1 and A2

Allele frequencies in
1
p = 0.49 + 2 (0.42) = 0.7
offspring gene pool p = frequency of allele A1
have not changed from parental
q = 12 (0.42) + 0.09 = 0.3 to offspring generation.
q = frequency of allele A2 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
 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

Source population New population Source population New population

Seed
Gene
flow

A1A1 A1A1 A1A2 A1A1 A1A2 A1A1 A1A1 A1A2

A1A1 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 Gene flow causes allele

are very different 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 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 For example, directional selection caused average body
a trait. size to increase in a cliff swallow population.
Normal distribution Original population
(N = 2880)

Before selection
Survivors
(N = 1027)

Change in
average
Low High value
fitness fitness
During selection

Change in
average
After selection value
Figure 25-4

Stabilizing selection reduces the amount of variation For example, very small and very large babies are the
in a trait. most likely to die, leaving a narrower distribution of birth
weights.
Normal distribution

Before selection Mortality

Heavy
mortality
on extremes
Low High fitness Low
fitness fitness
During selection

Reduction
in variation
After selection
Figure 25-5

Disruptive selection increases the amount of variation For example, only juvenile black-bellied seedcrackers that
in a trait. had very long or very short beaks survived long enough to
breed.
Normal distribution

Before selection

Only the Only the

extremes extremes
survived survived
Low fitness
High High
fitness fitness
During selection

Increase in
variation
After selection
Artificial Selection
 AKA: Selective Breeding
 Humans, not the environment selects
for the traits found in organisms
 Ex: Dog breeding, agriculture,
samurai crabs:
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 to diverge due to drift and isolated from one another.
float to an island on a raft. selection.

VICARIANCE CAN ISOLATE POPULATIONS.

River

1. Start with one continuous
population. Then a chance
event occurs that changes
the landscape (river changes
course.)
2. Isolated populations begin 3. Finish with two populations
to diverge due to drift and isolated from one another.
selection.
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 Feeding
the fruit of on the
a nonnative fruit of
species a native
species

Nonnative fruits are much smaller than native fruits.

Nonnative plant Native plant

(small fruit) (large fruit)

Evidence for disruptive selection on beak length

Short-beaked Long-beaked population
population growing on native plants
growing on
nonnative
plants
Figure 26-8

Diploid parent Tetraploid parent

(Two copies of (Four copies of
each chromosome) each chromosome)
Meiosis

Haploid gametes Diploid gametes

(One copy of (Two copies 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
Individuals that look like
warblers
Townsend’s warblers but
(in red)
have hermit mtDNA

Some individuals
Townsend’s-hermit have Townsend’s
hybrid mtDNA, others
have hermit
Pacific Ocean 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
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 Male lions are larger than females lions and
beetle Dynastes granti use their elongated coloration in territorial and courtship have an elaborate ruff of fur called a mane.
horns to fight over females. displays.
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.

What disproved spontaneous
generation of life?
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)
Miller-Urey Experiment
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
Endosymbiosis
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  Animals evolved
 1st life forms  Plants and fungi
 Accumulation of colonized land
atmospheric  Land became
oxygen colonized by other
 1st eukaryotes organisms
 Multicellular
organisms