Evolution

Andrey Nikitin
June 2023

Table of Contents
1 Introduction 2

2 Evolution 2
2.1 Important Dudes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2.2 The Origin of Species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2.3 Types of Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
2.4 What is a species? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.5 Evolution on a Genetic Level . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.6 Types of Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.7 Hardy-Weinberg Equilibrium . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

3 Taxonomy 15
3.1 Important Dudes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

4 Cladistics 17
4.1 Clades . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.2 Taxons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.3 Maximum Parsimony . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

5 Conclusion 21

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1 Introduction
Humans are fascinated with the past. From a young age, we learn history, tell stories, and obsess
over dinosaurs. In a sense, understanding our past allows us to understand our present: past
events determine future outcomes and shape our lives. With this interest in the past, it is natural
to then consider the past of life itself: evolution. In this lesson, we will explore why things came
to be the way they are now.
For this handout:

• Key words will be bolded.

• Obscure info will be in gray.

• Examples will be in blue.

• Outdated info will be in pink.

2 Evolution
Since you’ve likely already heard lots about Charles Darwin and his theory of evolution by
natural selection, which he developed during his trip to the Galapagos islands aboard the
HMS Beagle, I will keep this section brief.

2.1 Important Dudes

Fossils provide information about organisms of the past. Thus, they were an important source of
evidence for Darwin to develop his theory.

• Georges Cuvier: The father of paleontology. He believed in punctuated equilibrium,

the idea that the Earth experienced rapid changes during brief cataclysmic events.

• James Hutton: Believed in gradualism, the idea that the Earth formed over gradual and
slow processes.

• Charles Lyell: The leading geologist during Darwin’s time. He supported Hutton’s gradu-
alism, saying that the same processes that shaped the Earth over millennia continue to act
today. This idea of slow, gradual processes creating change influenced Darwin’s ideas on how
evolution works.

There were other people who proposed theories for evolution:

• Jean Baptiste de Lamarck: Developed the theory of use and disuse (the idea that
organisms lose parts that they do not use and strengthen those that they do use) and inher-
itance of acquired traits (the idea that organisms experience changes over their lifetime
that they pass on to their children). The most common example is that giraffes have long
necks because their ancestors had to stretch their necks to reach food high up. Over time,
all this stretching made their necks longer, giving their children longer necks.

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Figure 1: Lamarck’s inheritance of acquired traits and theory of use and disuse explaining
how giraffes evolved longer necks. (Source: [Link])

His ideas were already questionable in his own time, but they serve as a good contrast to
Darwin’s theory.

• Alfred Russel Wallace: Darwin was reluctant to publish his theory. However, Lyell
warned him that someone else might come to a similar conclusion. That person ended up
being Wallace! Wallace independently came to the same conclusion as Darwin at the same
time. Although Wallace published his theory first, he respected Darwin and admired the
extensive research Darwin had done, so he allowed Darwin to take credit for the theory (so
wholesome!).

2.2 The Origin of Species

Charles Darwin developed his theory on evolution while touring the world on the HMS Beagle. In
the Galapagos Islands, Darwin noticed that on each island, the finch (a small bird) that lived
there had a beak uniquely suited to the food source present on that island. Darwin realized that
these adaptations were essential to understanding evolution, leading him to come up with the
following ideas:

• Members of a population often vary in inherited traits.

• All species produce more offspring than the environment can support, leading to many off-
spring dying and failing to reproduce.

• Individuals whose inherited traits give them a better chance of surviving and reproducing
in their specific environment will have more offspring than others. This idea is known as

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relative fitness, where the more fit you are, the more offspring you will pass your genes
onto.

• This unequal ability for individuals to reproduce will cause favorable traits to accumulate
over generations.

In other words, populations evolve, not individuals.

In his book, The Origin of Species, Darwin cited fossils and artificial selection of crops and
livestock by humans to support his theory. Instead of using the word evolution, Darwin called it
descent with modification.

2.3 Types of Evolution

We can describe the traits of species as either ancestral traits that they inherited, or derived
traits that they acquired to be better adapted to their environment.

• Divergent evolution: When a single species is split into two separate populations, their
shared ancestral traits will differentiate to better fit their new environment. This creates
homologous structures: they look different, but are actually the same.
The most common example is that the bones in the forearms of all mammals are the same,
although they all do different things.

Figure 2: Homologous structures in the mammalian forelimb.

(Source: Campbell’s 12th edition)

This can occur in two main ways:

– Allopatric speciation: The two populations are in different places (e.g. separated by
a new mountain).

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– Sympatric speciation: The two populations are in the same place, but for some
reason, they can not mate (e.g. active at different times of day, different mating rituals,
sexual organs are incompatible, etc.)

• Convergent evolution: When two different species adapt to the same environment. This
creates analogous structures: They look the same, but are actually different.
For example, the wings of a dragonfly are not the same as the wings of a bird, or a bat. They
all share a common environment or function (flying in the air), but since they are derived
from different ancestors, the structures are different.

• A structure that is no longer used by an organism will often become a vestigial structure,
a reduced remnant of what it once was. For example, whales and snakes still have a pelvis
(albeit a very tiny one) even though they do not have legs.

Example 2.1: (USABO Semifinals 2017)

Solution: The answer is C. As we saw earlier, the most common example of homologous struc-
tures is the bones of mammalian limbs. Also, you should notice that features shared by organisms
that are closely related tend to be homologous structures while those shared by organisms that
are not closely related (e.g. a dolphin is a mammal while a shark is a fish, so A is wrong) tend to
be analogous structures. If you read the biosystematics handout, then you will be able to develop
an intuition for which organisms are closely related.

Example 2.2: (USABO Semifinals 2017)

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Solution: Notice that answer choices A, B, and D all refer to new environments or geographic
isolation, which is indicative of allopatric speciation. Meanwhile, C talks about preventing hybrids,
which, as you will see in section 2.4, occurs when two species live in the same environment.
Therefore, C is an example of sympatric speciation and is the answer.

A special type of speciation occurs when new land is available (usual examples are a new
island from a volcano, or land from under a glacier is exposed as the glacier retreats), or a sudden
extinction leaves a lot of roles (niches) available in the environment.

• The first organism to colonize new land is called a pioneer species or founder species.

• From these first colonizers, species will rapidly adapt to fill all of the available niches. This
rapid increase in the number of new species is known as adaptive radiation.

Figure 3: Adaptive radiation in Darwin’s finches (Source: COVE)

2.4 What is a species?

A species can be defined in several ways. Here are a few of them:

• Biological species concept: A species is a group of populations whose members can inter-
breed. Two organisms are from different species if they can not produce viable offspring.

– While this definition is useful for seeing how speciation occurs, it fails to describe fossils
or asexually reproducing organisms.
– There are prezygotic barriers and postzygotic barriers that prevent organisms
from two different species from producing viable offspring.
– The offspring between two different species is known as a hybrid. Even though a hybrid
may survive, it is not a viable offspring because either it or its progeny will not be able
to reproduce.

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Figure 4: Barriers to reproduction between species. (Source: Campbell’s 12th Edition)

• Morphological species concept: A species is a group of organisms that have similar

morphological features.

– While this can describe fossils or asexual organisms, its criteria are subjective.

• Ecological species concept: A species is defined by its ecological niche, how the members
of the species interact with biotic and abiotic factors in their environment.

– While this definition accommodates asexual organisms, it considers organisms in differ-

ent environments that can interbreed to be separate species.

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Example 2.3: (USABO Semifinals 2017)

Solution: Notice how this question defines the lice based on where they live and how they affect
humans. In other words, the difference between head and body lice is their niche, so the answer is
D. Also, we can rule out B (since they look the same physically), and C (since they can interbreed).
A and E are irrelevant.

2.5 Evolution on a Genetic Level

The adaptations that natural selection acts on ultimately come from variations in the genome.
Each gene, comes in multiple variants called alleles. The change in the proportion of these alleles
is called microevolution.

A lot of new genetic variation comes from mutations. Many mutations, however, are silent
and produce no observable changes. This neutral variation is not acted on by natural selection
and thus serves as a useful molecular clock.

• Since mutations happen at a steady rate and natural selection does not affect these neutral
mutations, we can count the number of mutations between species to figure out how long
ago they diverged from their common ancestor! This process of determining evolutionary
relationships by counting mutations in the genome is known as molecular systematics.
(Systematics is the classification of organisms and molecular is anything involving DNA)

• rRNA is used for long periods of time

• mtDNA (mitochondrial DNA) is used for short periods of time and recent events.
(e.g. mapping human evolution)

• Homologous genes are important for showing evolutionary relationships. Although they
come from the same ancestor, the genes have accumulated mutations that make them differ-
ent. They are classified into two types:

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– Orthologous genes: This describes when an ancestral gene diverges into separate
species. The copies are orthologous to one another because they are in different species.
– Paralogous genes: This describes when an ancestral gene duplicates. Then, the two
copies of that gene diverge to perform different functions within the same species. You
can think of it as the two copies of the gene being parallel to one another since they are
in the same organism’s genome.

Figure 5: Two types of homologous genes. (Source: Campbell’s 12th Edition)

• When an individual passes on genes to its offspring, this is known as vertical gene transfer
(since the transfer occurs vertically on the tree of life from parent to child). However, it is also
possible for an individual to acquire genes from another organism that is not their parent.
Plasmids, transposable elements, viruses, and fusion can all result in this horizontal gene
transfer (since the transfer occurs horizontally on the tree of life between organisms that
do not share any recent ancestry).

2.6 Types of Selection

There are several types of selection that can occur depending on what traits are selected for:

• Directional selection: One extreme of the allele becomes unfavorable, causing the gene
pool to shift towards the other extreme of the allele. For example, when the Industrial
Revolution occurred in England, the light-colored bark of trees that peppered moths (Biston
betularia) camouflaged with were covered by black soot. As a result, the previously prominent
light-colored moths became easier for predators to spot. This caused a directional selection
in favor of darker moths.

• Disruptive selection: The intermediate version of the allele becomes unfavorable, causing
both extremes of the allele to be favored.

• Stabilizing selection: Both extremes of the allele become unfavorable, causing the inter-
mediate version of the allele to be favored.

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Figure 6: Types of selection. (Source: BioNinja)

Example 2.4: (USABO 2016 Opens)

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Solution: This scenario is a perfect example of directional selection. When the color of a vole
does not match its background, it is easier for predators to see and capture them. Therefore, when
the background is white, more white voles survive and pass on their genes, causing a directional
selection towards white color. When the background is red, more red voles survive and pass on
their genes, causing directional selection for the red color. Thus, the answer to 45 is B. The
answer to 46 is E, since more red survive and fewer white survive when the background is red.
Finally, 47 is A. The adaptation, in this case, is the coloring of the vole. These adaptations help
the vole to survive, resulting in directional selection.

• Balancing selection: This type of selection is rarer than the other three. Here, all versions
of the allele are equally favored, promoting diversity. There are two main instances where
this occurs:

– Frequency-dependent selection: This occurs when a trait is selected against more

the more prominent it is. For example, the scale-eating fish (Perissodus microlepis)
is either left-mouthed, attacking its prey’s right flank, or right-mouthed, attacking its
prey’s left flank. When left-mouthed fish become prominent, prey begins strengthening
their right side, selecting against left-mouthed and for right-mouthed fish. Then, the
opposite happens as right-mouthed fish become more frequent. Thus, the most common
phenotype oscillates between left and right-mouthed, keeping the frequency of each to
∼ 50% over time.
– Heterozygote advantage: A heterozygote genotype that presents an advantage for
a dominant/recessive phenotype displays balancing selection for the phenotypes. For
example, sickle-cell disease is often lethal for homozygous recessive individuals, yet
the harmful allele is still very frequent (15-20%). This is because heterozygotes display
increased resistance to malaria and thus are selected for, allowing the recessive allele to
continue to be common.

• Sexual selection: Certain traits are selected for to increase the chance of finding a mate.
There are two types:

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– Intrasexual selection: Individuals of the same sex (usually male) directly compete
with one another for access to the other sex. For example, the antlers on deer.
– Intersexual selection (mate choice): Individuals of one sex (usually female) select
mates of the opposite with a certain trait. For example, the showiness of peacocks.
– Sexual selection can result in sexual dimorphism, where one sex looks different from
the other.

There are also special terms for how the gene pool, the collection of genes of all individuals
within a population, changes.

• Gene flow: Genetic variation in a population due to immigration or emigration.

• Genetic drift: Genetic variation due to taking a small proportion of the population.

– Bottleneck effect: If a large portion of the population dies off, then only the survivors
will be able to pass on their genes. As a result, the population loses genetic diversity
and only represents a small portion of the gene pool expressed by the survivors.
This has happened to species hunted to near extinction, such as cheetahs.
– Founder effect: When an organism colonizes a new area, its genes will be the ones
that are passed on to the species that will inhabit the area. As a result, only a small
portion of the original gene pool is passed on.

Figure 7: Sources of genetic variation. Thus, they violate the Hardy-Weinberg Equilibrium.
(Source: BioNinja)

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2.7 Hardy-Weinberg Equilibrium

The Hardy-Weinberg equation is used to predict how allele frequencies will change over time.
However, there are several conditions that must be met in order for it to be applicable

1. No mutations

2. Random mating

3. No natural selection

4. Extremely large population size

5. No gene flow

Since Hardy-Weinberg assumes that the allele frequencies of the dominant p and recessive q
alleles remain constant, we can use them to determine phenotype frequencies.

Since an allele is either dominant or recessive, then p + q = 1 allows us to say the following is true:

(p + q)2 = 12 = p2 + 2pq + q 2 = 1

Thus, after sufficient time, we know the proportion of the population that is homozygous
dominant (p2 ), heterozygous (2pq), or homozygous dominant (q 2 ).

Example 2.5 (USABO Semifinals 2017)

Solution: This is one way questions can be asked about Hardy-Weinberg. Here, we are given the
genotypes and are asked to calculate allele frequency. The process for this is very simple. Each
organism has two alleles, so just count the number of times the allele shows up and divide by the
total number of alleles. There are 20 A1A1, so that contributes 20(2) = 40 A1 alleles and 0 A2
alleles. There are 50 heterozygotes, so that contributes 50(1) = 50 A1 alleles and 50(1) = 50 A2
alleles. There are 80 A2A2, so that contributes 0 A1 alleles and 80(2) = 160 A2 alleles. Therefore,
40 + 50 90 3
p= = =
2(20 + 50 + 80) 300 10

So, the answer is C.

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Example 2.6: (USABO Semifinals 2018)

Solution: This is the other way questions can be asked about Hardy-Weinberg. Here, we are
given allele frequencies and are asked to calculate how often a genotype shows up. Note that the
conditions described in the question satisfy those of Hardy-Weinberg equilibrium (large population,
isolated, immune to mutations, no natural selection). So, to find heterozygotes we simply do

2pq = 2(1 − .18)(.18) = 2(.82)(.18) = .2952

What?! This isn’t any of the answer choices! What went wrong? It turns out that this is
a sneaky question... Hardy-Weinberg is NOT satisfied because there is inbreeding, so there is
no random mating. There is a stigma against inbreeding in our society, and for good reason:
inbreeding concentrates the alleles by having similar genotypes mate with each other, resulting in
homo genotypes being more common than usual. This is why inbreeding is often associated with
the expression of unusual recessive traits, such as the Habsburg Jaw.

So, the answer to this question is A because heterozygotes are less common in inbreeding,
and A is the only answer choice < .2952

3 Taxonomy
Taxonomy is the study of how organisms are named and classified. In general, any level of
classification is a taxon.

The order of classifications from most general to most specific is: Domain, Kingdom, Phy-
lum, Class, Order, Family, Genus, Species. There are plenty of mnemonics available online
to help you remember this.

It is generally agreed that there are 3 Domains and 6 Kingdoms (Originally, there were 5
since Bacteria and Archaea were combined into a kingdom called Monera).

• Bacteria: this is both a domain and kingdom.

• Archaea: this is both a domain and kingdom.

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• Eukarya: this is the third domain, characterized by organisms with a nucleus in their cell(s).
Eukarya contains 4 kingdoms:
– Animalia: contains animals.
– Plantae: contains plants.
– Fungi: contains fungi (no, they are not plants).
– Protista: This is a catch-all category for anything that doesn’t fit into the other three
kingdoms.

Figure 8: Shows the order of taxons for a panther, with the most general at the bottom and the
most specific at the top. (Source: Campbell’s 12th Edition)

3.1 Important Dudes

Aristotle was the first person to attempt this, developing a hierarchy of classifications known as
scala naturae.
Carolus Linnaeus later used this idea to develop his binomial nomenclature, where each
organism is given a unique 2-part name consisting of their genus and species. He used Latin names
to avoid confusion in naming between different languages. His system is largely the same one we
use today.
Alternatives to binomial nomenclature have been proposed, like PhyloCode, which only names
groups that contain the common ancestor and all its descendants, but these are rarely used.

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4 Cladistics
In cladistics, phylogenetic trees are constructed to show the evolutionary history between
species. If a phylogenetic tree includes all descendants of a common ancestor, then it is rooted.
These trees contain branch points to show where two species diverged:

• Dichotomy: 2 species break off from the branch point.

• Polytomy: The evolutionary history is unclear, so more than 2 species break off from the
same branch point.

• A shared ancestral character is a trait that was acquired before the branch point and
should be present in all descendants.

• A shared derived character is a trait that was acquired after the branch point and should
only be present in those specific descendants. Derived traits are also called apomorphies
and are classified into different types based on which ancestors and descendants possess the
trait.

– Autapomorphy: A derived trait that is unique to that taxon.

– Synapomorphy: A derived trait shared by two or more taxa and is believed to also
have been present in their common ancestor.
– Symplesiomorphy: An ancestral trait shared by two or more taxa.
– Homoplasy: An ancestral trait that, due to convergent evolution, has been indepen-
dently lost or gained in multiple taxa.

Figure 9: Different ways derived traits can appear in a phylogenetic tree. (Source: Wikipedia)

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4.1 Clades
A grade is any group that shares similar features (but not necessarily an evolutionary relationship).
Meanwhile, a clade is a group that shares common ancestry, and they come in 3 main types:

• Monophyletic: includes the common ancestor and all descendants.

• Paraphyletic: includes the common ancestor but not all descendants.

• Polyphyletic: includes members from multiple different ancestors.

Figure 10: Types of clades. (Source: Campbell’s 12th Edition)

Note that all of the phylogenetic trees above are rooted, since they clearly define what the
common ancestor of all the taxa present is. You can tell if a tree is rooted if there is a line that
does not lead to an organism (in this case, it is the line on the very left). In addition, these trees
are ultrametric because all of the descendents are the same distance from the common ancestor
(e.g. everything lines up nicely on the right).

4.2 Taxons
We can also organize a phylogenetic tree by its taxons:

• Sister taxa: Two taxa that share an immediate common ancestor.

• Basal taxon: The earliest diverging species.

• Ingroup: The organisms in question that we are studying.

• Outgroup: A species that diverged before the lineage of the ingroup.

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Example 4.1: (USABO Opens 2018)

Solution: For a phylogenetic tree, orientation and (for most) length of the lines do not matter.
The only thing that matters are the branch points, which show common ancestry. Thus, we want
to find a tree that has a different branch point. By inspection, answer choice A has F and H as
sister taxa while every other tree has F and G as sister taxa. Therefore, the answer is A.

Example 4.2: (USABO Semifinals 2015)

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Solution: The answer to 58 is D because that is where E first branches off from the rest of the
tree.
For 59, let’s consider each choice. A is wrong because the tree is rooted: the line at the very
bottom shows that it is the common ancestor of all species present since it does not lead to any
organism. B is wrong because the tree is not ultrametric: the species do not line up neatly at
the top. C is the correct answer because 5 is only present in E, and is thus unique to that
taxon. D is wrong because D is at the top of the tree, indicating it is alive in the present day. E is
wrong because to figure out how related two organisms we can count the number of branch points
between them. C and B have have 2 branch points (1,2) between them, while A and D have three
branch points between them (1,2,3). This means that A and D are more distant than B and C
are.
For 60, we just want to make a monophyletic group, which includes all descendants and their
common ancestor. A, B, and E all work. C and D are wrong because if you have E, which is
the basal taxon in this scenario, then you must have all the other species.

4.3 Maximum Parsimony

Maximum Parsimony is the same principle as Occam’s Razor - the simplest explanation is
often the best. As a result, we tend to construct trees that minimize the number of changes,
since it is far more likely that a trait evolved in a common ancestor and was passed on to all its
descendants rather than the trait evolving independently in each of the descendants.

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There are two main concepts related to this:

• Maximum likelihood: Determines what is most likely based on the probability of changes
in the DNA sequence.

• Phylogenetic bracketing: We can predict by maximum parsimony that if closely related

organisms share a trait, then their common ancestor likely also had the trait. This isn’t
always true but is instead an assumption that should be tested.

5 Conclusion
In conclusion, we have seen how the forces of natural selection have shaped species to evolve into
the organisms they are today. In fact, we can even predict what the future makeup of populations
will look like using the Hardy-Weinberg equation. This handout mainly discussed the theory
behind evolution. If you wish to see how organisms actually relate to one another with plenty of
examples, then check out the biosystematics handout!

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