Domain 1: Evolution

1.1: Natural selection is a major mechanism of evolution.

(EK1.A.1)

1. Natural Selection
Darwin/Historical Evolutionary Development

Historical development of evolutionary thought pre-Darwin

Lyell- Geology, Uniformatarianism! very old earth.
Malthus- Exponential Population Growth
LaMarck- Evolution. Inheritance of acquired characteristics (wrong, but still
evolutionary)

Darwin- Uninspired youth. Ships naturalist on board HMS Beagle.

Circumnavigation of the globe. Return to Europe and delay publication of theory
until pressed by Alfred Russell Wallace.

Natural Selection:
Inherent Variation in all organisms.
Overproduction of Offspring (Malthus)
Differential success (fitness) of different variants in survival and reproduction
(adaptations).
Inheritance of adaptations leads to populations becoming better adapted for the
environment over time.

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Repeat for millions of years.

Fundamental conclusions:
Ancient age of the Earth (billions of years, not thousands)
Common Ancestry of all organisms on Earth (tree thinking).

Unsettled by Darwin:
Origin of Life
Origin of species
Nature of variation/inheritance

2. The Modern Synthesis

Connection of evolution to change in allele frequencies in populations/ basic
mathematical analysis.
The Modern Synthesis- connecting Darwinian evolution to genetics and
modern understanding of inheritance.

Traits are the result of genetic instructions in DNA (genes)

Variations in traits are the result of changes to genes (mutations)

alleles: different variants in traits

Evolution: Changes in allele frequencies over time.

Example: Galapagos Finches/Grant Studies

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Studies of finch populations on an isolated island in the Galapagos.
Measurements of the beak dimensions of all birds on the island every year for
decades.
Able to connect changes in beak dimensions to fluctuations in the environment
(precipitation, seed sizes)

Relevant Misconceptions:
Evolution is a population level phenomenon. The evolution of a population
emerges from the individual fitness of members of that population. As they
survive and reproduce, or not, the frequencies of alleles in the next generation will
change accordingly.

1.2: Natural selection acts on phenotypic variations in

populations. (EK1.A.2)

1. How Natural Selection Works.

Connection of Phenotype to Genotype (Basic Central Dogma)
Genotype: The alleles that an individual has for a particular trait.
Homozygous: Two copies of the same allele.
Heterozygous: Two copies of different alleles for each trait.

Why do we have two alleles for each trait? Because of sexual reproduction.

Phenotype: The trait that an individual shows.

Genotype determines phenotype.

Alleles control the production of proteins and the proteins determine traits

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Dominant vs. recessive alleles- some alleles (dominant) will control phenotype
over other alleles (recessive) when both are present.

Example: Eye color (simplified)

Two alleles: Brown (B) and blue (b). Two phenotypes: Brown eyes and blue eyes.
Individuals who are homozygous will either have brown (BB) or blue (bb) eyes.
Brown is dominant and blue is recessive, so heterozygotes will have brown eyes.

Relevant Misconception:
Dominant alleles are better than recessive alleles: Dominant and recessive have
nothing to do with their effect on fitness. They only refer to how they contribute
to phenotype expression.

Relationship between phenotype and fitness:

Different phenotypes will be more or less fit, depending upon the requirements of
the environment.

Fitness: Ability to contribute genes to the next generation (reproduction).

The environment determines fitness, and fitness may change as the environment
changes.

Example: Pesticide Resistance

Individuals who are resistant to a pesticide will be more fit than individuals who are
not when the pesticide is present in the environment. If there is no pesticide

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 present, resistance will not contribute to fitness (may detract, depending on the
nature of that resistance).

Human impact on variation:

Humans are able to impact variation in other organisms by controlling which
individuals are able to reproduce.

Artificial selection: When reproductive success is determined by human

requirements

Examples: Dogs, monocrop fields

1.3: Evolutionary change is also driven by random processes.

(EK1.A.3)

1. Other Evolutionary Forces

Genetic Drift:
The random, non-selective, changes in allele frequency due to chance events.
Genetic drift has a larger effect on smaller populations, since each individual is a
larger percentage of the total alleles in the population.

The Founder Effect:

When the descendants of a small, founding population have different percentages of
alleles than the population that the founders came from.

Example: The rate of polydactyly in the Amish population is higher than it is in the
European population that the Amish came from.

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The Bottleneck Effect:
Following a catastrophic decrease in a population, the survivors of the bottleneck
event may have a different percentage of alleles than the pre-bottleneck
population.

Example: The Cheetah population underwent a major bottleneck during the last ice
age (and subsequent hunting). Any two cheetahs are genetically equivalent to
identical twins.

Gene Flow:
The intermixing of alleles from two overlapping populations. This frequently leads
to an equalizing of differences in allele frequencies between populations.

Example: The effect of human migration on population characteristics since the

industrial revolution.

Sexual Selection:
Selection for characteristics that aid an organisms reproductive success. Often
these characteristics may seem maladaptive for the individual.

Examples: Peacocks (intersexual), dominance competitions (intrasexual)

Relevant Misconceptions:

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 Evolution is a random process: Evolution is a change in allele frequencies over
time. There are random evolutionary processes (genetic drift) and non-random,
selective processes (natural selection).

1.4: Biological evolution is supported by scientific evidence

from many disciplines, including mathematics. (EK1.A.4)

1. Evidence of Evolution

Geographical/Geological Evidence:
Radiometric dating enables the age of fossils and rock layers to be determined and
establishes the age of the Earth as ~4.5 billion years.

The appearance of similar fossils on different continents correlates to the

positions of those continents over geologic time, accounting for continental drift.

The fossil record establishes a history of life on Earth. There are no

anachronisms in the fossil record. Fish show up millions of years before
mammals.

Living organisms resemble fossilized, extinct forms.

Fossilized organisms showing major evolutionary transitions between groups are

found with regularity.
Example: Tiktallik

Anatomical Evidence:

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 Similarities and differences in the anatomy (morphology) of organisms provide
evidence/clues to how they have evolved.

Vestigial structures: Structures that have lost their primary adaptive purpose.
Example: Whale hind limbs

Homologous structures: Structures present in a common ancestor, which have

diverged during evolution.
Example: Vertebrate limbs.

Analogous structures: Structures that have evolved multiple times in different

lineages to fill similar adaptive needs.
Example: Wings

Chemical Evidence:
Similarities and differences in DNA and protein sequences. As lineages diverge,
they will accumulate mutations in DNA sequences, which will alter the sequences
of proteins.

Mathematical Modeling:
Computational analysis of evolution: The ability to analyze large amounts of
chemical sequence data to establish evolutionary relationships among organisms.

Hardy-Weinberg Theory: The ability to quantify the amount of evolutionary

change from generation to generation to determine how evolution is affecting the
population.

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2. MATH Skills: HW Theory

Hardy-Weinberg equations enable us to determine how much a population is

evolving from generation to
generation.

Hardy-Weinberg equilibrium: Refers to an idealized, non-evolving population.

Five characteristics:
Large size (no genetic drift)
Random mating (no sexual selection)
Stable environment (no natural selection)
No immigration/emigration (no gene flow)
No mutations.

No real population is in HW equilibrium.

Two equations (for a trait controlled by two alleles, where p is the dominant allele
and q is the recessive allele):
Gene pool equation: p + q = 1

p = frequency of dominant allele, q= frequency of recessive allele

Organism equation: p2 + 2pq + q2 = 1

p2 = frequency of homozygous dominant individuals, 2pq = frequency of

heterozygotes, and q2 = frequency of homozygous recessive individuals

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To solve HW equations, always determine the frequency of recessive individuals first,
and use that to solve the rest of the equation.

Sample problem: In pea plants, the allele for purple flowers is dominant to the
allele for white
flowers. If 99% of the plants in the population have purple flowers, determine
the percentage of heterozygotes in the population.

Solution: Given: 99% (.99 frequency) have purple flowers. Cant say how much are
p2 and how much are 2pq. But we do know that p2 + 2pq + q2 = 1, and that in this
case p2 + 2pq = .99. So we can solve for q2, which is .01 (1 percent). Now we
solve for q, by taking the square root of .01 which is .1 (square root weirdness in
decimal land!). If q is .1, than p = 1 - .1, or .9 (90 percent). Now that we know
that, we can solve for the frequency of p2 which is .92 = .81, and the frequency of
2pq, which is 2*.9*.1 = .18. So 18% of our population are heterozygous for
flower color.
If the data in a HW problem does not add up to 1, then the population is NOT in
HW equilibrium.

Uses of HW equilibrium:
To determine how a population is evolving from generation to generation. (Is the
population out of HW equilibrium? Are the p and q frequencies changing over
generations?)

To help to determine which evolutionary pressures are affecting a population

more/less.

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1.5: Organisms share many conserved core processes and
features that evolved and are widely distributed among
organisms today. (EK1.B.1)

1. Evidence of Common Ancestry

Genetic Code:
All cellular organisms use DNA to store genetic information, expressing that
information through RNA in to protein structure.

The genetic code that translates nucleic acid into protein structure is essentially
universal among all lineages of life.

Metabolic Pathways:
All cellular organisms produce usable energy through similar metabolic pathways.

Example: glycolysis is the first energy producing metabolic pathway in essentially

every cell on the planet.

Cellular Morphological similarities:

All cells on the planet are structured on one of two major organizational plans.

Prokaryotes: Cells that lack any internal membrane-enclosed compartments

(organelles)

Eukaryotes: Cells that contain a variety of internal organelles.

Endosymbiosis:

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 The theory that major eukaryotic organelles (mitochondria and chloroplasts)
evolved from free-living prokaryotic cells that were engulfed and internalized by
eukaryotic ancestors.

Evidence: DNA sequences, reproduction patterns, double membrane structure.

1.6: Phylogenetic trees and cladograms are graphical

representations (models) of evolutionary history that can be
tested. (EK1.B.2)

1. Phylogeny
Phylogenetic tree/cladogram construction:
A cladogram is a diagram that groups items according to the number of traits that
they have in common:
The number of characteristics that are shared among the items are determined.
The items are then arranged in a tree diagram to represent these similarities.

A phylogenetic tree is a cladogram that groups organisms according to the number of

evolutionary traits that they have in common.

Characters/Sequence Data:
To construct a phylogenetic tree, either shared derived characters are used (traits
that are representative of the evolution of the organisms), or the amount of
similarity in DNA/protein sequence information is looked at.

Examples: vertebrate tree, whole life tree.

Phylogenetic tree construction:

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Determine similarities among organisms (character table works well).
Arrange organisms in a tree diagram showing simplest possible evolution.

Maximum parsimony: All else being equal, a trait is assumed to only evolve once and
be present in all of the descendant organisms.

SKILL Create A Tree: Selected Vertebrates

Animal Opposable 4-chamber Amniotic lungs Spinal
Thumb heart egg column

Chimpanzee 1 1 1 1 1

Mouse 0 1 1 1 1

Turtle 0 0 1 1 1

Frog 0 0 0 1 1

Fish 0 0 0 0 1

Lamprey 0 0 0 0 0

Continual revision:
As more data is gathered, the phylogenetic relationships among organisms are
continually revised to incorporate that data.

Role of computers:

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 Computer analysis is needed to determine the similarities in DNA/protein
sequence information, as the amount of data is beyond the human capacity to
analyze quickly.

1.7: Speciation and extinction have occurred throughout the

Earths history. (EK1.C.1)

1. Speciation Concepts
Species concepts:
Not discussed by Darwin.

Biological Species: A group of organisms that are capable of successfully

reproducing with eachother. Its testable!

Certain limitations (bacteria? Triceratops?): Have resulted in other definitions of

the term.

Speciation rates:
How quickly do new species evolve?

Gradualism: species are the product of slowly accumulating, small evolutionary

changes.

Punctuated equilibrium: species undergo long periods of very little change, followed
by rapid, large evolutionary changes.

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Evidence for both.

Example: Major Extinctions- eventually all species go extinct. There are several
periods of greatly increased rates of extinction through the fossil record.
Following these Mass extinctions, the species that survive quickly diversify and
occupy the vacated niches left open.

Adaptive radiation:
When one species evolves in to many species that occupy a variety of available
niches. Common after Mass extinctions (consider the mammals after the
dinosaurs), or when organisms are isolated on islands (consider the Galapagos
finches)

1.8: Speciation may occur when two populations become

reproductively isolated from each other. (EK1.C.2)

1. Speciation process

Reproductive Isolation:
If a species is a group of interbreeding organisms, than speciation occurs when a
group of organisms can no longer breed with any other individuals.

Does the speciation occur when the organisms are physically separated from their
parent population (allopatric), or does it occur when the organisms are physically
in contact with their parent population (sympatric).

Species Barriers:
Anything that separates one species from another:
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Pre-zygotic Barriers: Prevent gametes from combining into a fertilized zygote
Physical Barriers- geographical
Temporal Barriers- time of day/seasonal
Behavioral Barriers- mating rituals
Mechanical Barriers- incompatibility of reproductive structures
Chemical Barriers- incompatibility of proteins on gametes

Post-zygotic Barriers: Prevent the hybrid zygote from becoming an organism

capable of reproducing
Reduced viability- Hybrid is frail
Reduced fertility- hybrid is sterile
Loss of hybrid characters- hybrid loses hybrid traits over generations.

Examples: Mules, Apples, Fruit Fly Food Preference Study.

1.9: Populations of organisms continue to evolve. (EK1.C.3)

1. Ongoing evolution of organisms

Ongoing evolution of organisms:
Evolution is an ongoing process that can be observed and studied in currently
living populations of organisms.

Examples:
Pesticide resistance: The application of pesticides to crops drives the evolution of
pesticide resistance among pest organisms, which requires increased pesticide in
subsequent applications.

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Rock Pocket Mice: Coat coloration evolution has been driven by differences in the
rock coloration where the populations live. Different black populations have
evolved different mechanisms of melanin production (convergent evolution)

HW eq. applications:
HW Equilibrium can be used to analyze how a population is evolving from one
generation to the next.

1.10: There are several hypotheses about the natural origin of

life on Earth, each with supporting scientific evidence.
(EK1.D.1)

1. Origin of life
Nature of science re: Testable hypotheses for lifes origin.

Two Major hypotheses.

Panspermia: Life has an extraterrestrial origin, arriving on a meteor or similar

delivery system

Abiogenesis:
The origin of living systems from non-living components. A scientific hypothesis
because it provides testable predictions. Four major milestones for life to
develop from non-life:
Development of the chemicals that living systems are made of.
Encapsulation of those chemicals into isolated systems.
Development of an information storage molecule that can be inherited.
Reproduction of living systems.
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RNA world:
The hypothesis that RNA preceded DNA. Due to RNAs double function in
living systems as an information storage molecule and a catalytic molecule.

Evolution of metabolic pathways:

The development of the major ways that living systems process matter and energy.
Glycolysis is thought to have evolved first, as all modern living systems use it as
the first energy production pathway. Photosynthesis evolved later, leading to the
oxygenation of the atmosphere. Aerobic cellular respiration evolved last, as it
requires atmospheric oxygen to be accomplished.

Endosymbiosis:
The origin of eukaryotic cells from prokaryotic ancestors. Free-living ancestors of
eukaryotic mitochondria and chloroplasts were engulfed by eukaryotic ancestors,
and a symbiotic arrangement was established. Supported by a lot of evidence.

Evolution of multicellularity:
Multicellular organisms are able to specialize the structures and functions of their
cells to occupy niches that are unavailable to unicellular organisms. Many
unicellular organisms have multicellular life stages, and the systems that
multicellular organisms use to coordinate and communicate among their cells are
evolved from systems that are present in unicellular organisms.

Deep Time Considerations:

Approximate evolutionary dates (based on current evidence):

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 Formation of the Earth: 4.5 bya
Origin of life: ~4 bya
Origin of Photosynthesis: 3 bya
Origin of Eukaryotes: 2 bya
Multicellular life: 1 bya
Origin of Animals: 600 mya

1.11: Scientific evidence from many different disciplines

supports models of the origin of life. (EK1.D.2)

Discussion 1: Evidence for the Origin of Life

Geological evidence (Dating, Banded Iron, etc.):
Radioisotope dating allows us to establish the approximate age of fossil evidence.

Different events in lifes history have left geological evidence:

Banded Iron formations: Deposits of Iron Oxides that coincide with the
hypothesized origin of photosynthesis.
Fossil Fuels: Massive deposits of fossilized plants and other producers from the
Carboniferous period.

Miller-Urey Experiments:
Starting with simple chemical building blocks, in conditions that were
hypothesized to approximate early earth conditions, simple organic molecules
were produced (step 1 of abiogenesis). This finding has been replicated in a
variety of experimental conditions.

Commonalities of all organisms:

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The commonalities among all living systems support evolutionary descent from a
single common ancestor. It is the simplest hypothesis to explain the observation.

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