Copyright © Fall2024, Dept.

of Integrative Biology, UC Berkeley

Phylogenetics of Primates
Part I – Mammal Order: Primates
As you saw in the pre-lab video, tarsiers are weird. They have long been a puzzle to
evolutionary biologists, because they are obviously primates, but what kind of primate are
they? Humans are primates, too. Is the tarsier a close relative? The goal of this week’s lab is
to determine which group of primates the tarsier is most closely related to using
phylogenetic methods to reconstruct their most likely evolutionary history.

Figure 1.1 A tarsier.

Mammals are a group of vertebrates that can be distinguished by different characters, such
as mammary glands, fur, and three middle-ear bones. A primate is classified as one of the
Orders belonging to the Class Mammalia. All primates share distinctive similarities:
opposable thumbs, flattened faces, rounded crania, and flexible joints that allow for a larger
range of motion in the arms and legs than in other mammals. Primates are also heterodont,
meaning they have teeth differentiated for distinct functions, such as molars for crushing
and grinding, incisors for nipping or grooming, and canines for biting or intrasexual
display. Most mammals have nipples, either in rows along their bodies (like a cat nursing
her kittens), or on an udder at the back end (like a cow nursing a calf). Primates, however,
have pectoral nipples, a feature shared only with the elephants (Proboscidea), which nurse
their young under the forelegs, and the bats (Chiroptera), which wrap the young in their
wings and nurse upside down!
Primate clades
What are the different kinds of Primates? Traditionally, the Primates have been divided
into four major groups:
1) The lemurs and lorises: These primates are restricted mostly to Madagascar and
isolated pockets of Southeast Asia.

Page 1 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

Figure 1.2. Lemurs, like the ringtail lemur and the sifaka, are found only on the African island of
Madagascar. Lorises can be found in rainforest habitats in India, Sri Lanka, and some isolated populations
in Southeast Asia. Some loris species secrete a venom that they rub into their fur to deter predators.

2) The Catarrhines: These primates live in Africa and Asia, and are considered
monkeys. The name Catarrhine means “hooked” or “split-nose”, and refers to their
downward-pointing nostrils. These monkeys are generally terrestrial, living on the
ground in large troops. They walk on flat palms of all four feet. Males often have
exaggerated secondary sexual characters, like large canine teeth used in dominance
displays, colorful faces, and thick shaggy manes to protect them in combat with
other males. This group includes baboons, macaques and mandrills.

Figure 1.3. Catarrhines, like baboons, are primarily terrestrial and walk on their flat palms. Male mandrills
have brightly colored faces and large canine teeth to display their status in the troop. Found in Africa and
Asia, these monkeys have downward-pointing nostrils.

3) The Platyrrhines: These primates are also considered monkeys. The name
Platyrrhine means “flat-nose”, and refers to their nostrils flaring out to either side.
These monkeys are found in Central and South America, are arboreal (live in trees),
and have prehensile tails (tails that can act like a fifth limb, grasping branches).

Page 2 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

They eat primarily leaves and fruits, and live in smaller groups. Squirrel monkeys
and howler monkeys are Platyrrhines.

Figure 1.4. Platyrrhines, like the spider monkey, are arboreal and have prehensile tails that can grasp branches like a
fifth limb. The nose in all platyrrhines, like the squirrel monkey, have outwardly-flared nostrils. These monkeys are
found in Central and South America.

4) The Apes: These primates are not monkeys. Apes include us, Homo sapiens. We are
the only truly bipedal ape, walking upright on our hind limbs. The other apes have
large body sizes, and use the knuckles of their hands to support their weight when
walking, rather than using their palms. Most non-human apes are critically
endangered due to habitat loss and poaching. Gorillas, chimpanzees, orangutans and
siamangs (gibbons) are all apes.

Figure 1.5. Apes walk on their foreleg knuckles, rather than on flat palms. All primates have “thumbs” adapted to
grasping tree limbs. The hands of the other apes are similar to our own.

Where does the tarsier fit into this scheme? Tarsiers are so odd-looking that it seems like
they should be closely related to lemurs or lorises. Like lemurs, tarsiers can leap between
trees, and are nocturnal, like lorises, with enormous eyes that help them see in the dark.

Page 3 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

But there’s a problem with grouping organisms

just by similarity in appearance or behavior.
Because habitats select for similar adaptations in
very different organisms (an example of
convergent evolution), organisms that look
alike may not be closely related at all.
Early taxonomists fell into this trap, grouping
armadillos (a mammal) with turtles (a reptile).
Other early naturalists grouped orcas (a toothed
whale) with sharks (which are fishes), and
grouped bats (flying mammals) with birds!
Figure 1.6. Tarsiers have the largest eyes relative to their body size of any mammal.

Part 2 – Phylogenetics
Check out this great resource for understanding phylogenetics: Evolutionary Trees – A Primer
Phylogenetics is a better way to determine how organisms are related to one another,
because it is based on the evolutionary processes that gave rise to different taxa. (A note
here, taxon simply refers to a group of related organisms, and the plural form is taxa.
Taxon/taxa is a generic term that can be used to refer to species, genera, families, or any
other level of biological classification). All living things are related by common ancestry.
Therefore, any group of taxa that we could assemble shares an evolutionary history. A
phylogeny is a hypothesis about the evolutionary history of a group of taxa.
We can use many different kinds of evidence to help us answer questions about how
different organisms evolved. In today’s lab about tarsiers, we will use two types of data:
1) morphological data: anatomical characters, gathered by comparing homologous
structures such as bones, teeth, and other tissues from different taxa. Homologous
structures are structures inherited from a common ancestor.

2) molecular data: gathered by sequencing the homologous gene in DNA from

different taxa. We will be using a gene that codes for one of the subunits of the
hemoglobin molecule.
Although we know that any group of taxa shares a true evolutionary history, we can never
reconstruct the past with total certainty (this is especially true if we are dealing with
events that took place millions of years ago). Therefore, although we have very effective
methods for determining phylogenies, we can never know the phylogeny of a group of taxa
with total certainty. Our determination of the phylogeny of a group of taxa serves as a
hypothesis, subject to revision if additional evidence comes to light.
Hypotheses of phylogenetic relationships are represented by tree diagrams—the
branching patterns reflect a hypothesis of how different taxa are related to one another.
The tree diagrams are also called cladograms. Speciation produces new branches on the

Page 4 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

tree of life, while extinction removes branches from it. The cladograms group taxa by
common ancestry, from the smallest group of two sister taxa, to larger groups, sometimes
composed of thousands of species. Biologists attempt to group organisms into clades,
lineages that contain a common ancestor and all of its descendants. Clades are also called
monophyletic groups.
Smaller monophyletic groups can be subsets of larger monophyletic groups. We refer to
smaller groups contained within larger groups as being nested within the larger group. For
example, as mentioned above, birds are a monophyletic group nested within the larger
monophyletic group called reptiles. Reptiles are a monophyletic group nested within a
larger monophyletic group called vertebrates, and so on.

Figure 2.1. Example of a phylogenetic tree and challenges in reconstructing evolutionary histories.

The two taxa that branch from a common

ancestor are sister taxa. Ancestors are
represented on evolutionary trees as nodes.
Therefore, each node identifies a pair of sister
taxa, which are each other’s closest relatives.
Whether other taxa are nested within a sister
taxon (like smaller boxes fitted inside larger
boxes) does not change the sister relationship.
For example, in the cladogram shown in Figure
2.2, three nodes are numbered and seven extant
(living) taxa are labeled with letters. The sister
taxa identified by node 1 are B and C. The sister
taxa identified by node 2 are A and B+C.
Figure 2.2 Cladogram showing the evolutionary relationships among
seven hypothetical taxa (represented by letters A–G). Three nodes are numbered.

When relationships are well-understood, the branching pattern of a tree is assumed to be

bifurcating (two branches diverge from one another each time the tree branches).
However, when we are uncertain about the evolutionary relationships between groups, we
collapse the branches into a polytomy, where more than two branches originate from a
single point (or, "node”).

Page 5 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

Returning to the topic of phylogenetic groups, if you were to construct a phylogenetic

group consisting of a node and all of the descendants that branch from that node, you
would have created a monophyletic group (i.e., clade).
Which types of characteristics are useful for reconstructing evolutionary histories? An
important step is to identify homologous characteristics. These are the characters (DNA
sequences, morphological structures, patterns of development, or behaviors) that are
shared among taxa because they were inherited from a common ancestor. A character
state is a version of a character that we observe in organisms. For example, if eye color is a
character, then blue, black, brown and hazel might be the character states. With respect
to DNA, each nucleotide position in a DNA sequence is considered a character; the five
possible character states are the four types of nucleic acids that make up DNA (A, C, T, G) or
a gap in the sequence (a missing nucleotide). So, the number of characters in a DNA
sequence is its particular length (the number of nucleotides in the sequence), but the
number of character states is always five.
Character states that are shared by taxa but that are not inherited from a common ancestor
are called analogous traits. Analogous traits are not useful for reconstructing evolutionary
history, because they do not give any information about shared ancestry. For example,
forelimbs that are modified into wings in birds and forelimbs that are modified into wings
in bats are analogous because their most recent common ancestor did not have forelimbs
modified into wings; the state of having wings does not tell us anything about their shared
ancestor or the evolutionary relationship between birds and bats, because wings evolved
independently in the two lineages. If the presence of wings was the only shared trait we
used to infer patterns of common ancestry, we would make the mistake of suggesting that
bats are more closely related to birds than bats are to other mammals, which evidence
from many other characters clearly indicates is not the case. Thus, building cladograms
with datasets that include many characters helps prevent incorrect inferences caused by
analogous traits. A major benefit of molecular datasets is that they include many characters
because each nucleotide is potentially another informative character.
For each character you examine, you need to determine the ancestral and derived
character states. How can you do this without already knowing the evolutionary history?
You must select an appropriate outgroup (a taxon that is related to the taxa of interest) to
compare with the ingroup (the taxa of interest). All of the members of the ingroup should
be more closely related to one another than any are to the outgroup. The key assumption
here, which is reasonable but not infallible, is that the character states of the outgroup are
ancestral, and that the character states present in the ingroup (not the outgroup) are
considered to be derived. Although the character states of the outgroup are treated as
ancestral, an outgroup itself is not an ancestor of the ingroup; it could, however, be a sister
group, the group most closely related to the entire ingroup.

Page 6 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

Figure 2.3. The Hispaniolan solenodon (Solenodon paradoxus) is found only on Hispaniola. Morphologically, this
species closely resembles mammals living at the time dinosaurs inhabited the Earth. During the lab, you will use
the solenodon as an outgroup to the primates.

A derived character state that is shared by at least two taxa because of common ancestry is
called a synapomorphy. By definition, synapomorphies are inherited from a common
ancestor. Therefore, they are homologous characters.
To perform a phylogenetic analysis, character states are coded into a character matrix, a
table that aligns homologous characters for an outgroup and members of the ingroup.

Figure 2.4 (A) Venn diagram grouping taxa by shared characters. (B) Cladogram depicting the same relationships and
evolutionary history. The evolution of each character has been marked onto the tree with hash marks.

Page 7 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

Figure 2.4 is an example of how to construct a phylogeny of tetrapods, the four-limbed

vertebrates. The outgroup in this example is sharks; they are more distantly-related
vertebrates. The absence of hind limbs is coded as “0” because this state is ancestral, and
the presence of hind limbs is coded as “1” because possessing hind limbs is the derived
state.
Notice that all the taxa have the ancestral condition of 0 for the “vertebrae” character.
Having vertebrae is the ancestral condition for these organisms, and because all of the
organisms in the matrix have the same character state, the character of “vertebrae” is not
informative. It does not tell us anything about how these animals are related to one
another.
“External pouch” and “feathers” each appear in one taxon only. These characters are
derived, but not shared between multiple taxa (they are each in one taxon only). Therefore,
these characters are not informative for grouping taxa.
In summary, neither ancestral characters nor derived characters that occur in only
one lineage are informative for grouping taxa.
We can put other types of data into a character matrix as well. In Figure 2.5, we have lined
up DNA sequences for the same gene for three different species. When we choose genes for
phylogenetic analyses, we tend to look for genes that are similar enough across taxa to
have some parts of the gene that are the same and other parts that vary among taxa. In
other words, we choose genes in which unique mutations have accumulated in each taxon
over the time the taxa have been diverging. Genes for proteins like insulin, cytochromes,
glycolysis enzymes, and muscle proteins tend to be very similar across very different taxa,
telling us that the states of these genes and the proteins they produce are important to the
physiology of organisms.
In Figure 2.5, you can see that characters (loci) 1, 5 and 7 are not informative, because they
are identical in all three taxa. The gaps, identified by hyphens, indicate places where there
have been mutations. For example, either Species C has had a nucleotide deleted at Locus
2, OR species A and B have both had a T inserted at Locus 2. (A deletion is a type of
mutation that eliminates parts of a DNA sequence; an insertion is a type of mutation that
inserts one or more nucleotides into a DNA sequence).

Figure 2.5. A character matrix for DNA sequences of the same gene collected and sequenced from three different
species. In this example, there are 7 characters, and five possible character states (A, T, G, C, and gap).

Page 8 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

It is important to realize that when you construct an evolutionary tree you are proposing a
hypothesis. When biologists build trees, they do not initially know the order in which
characters evolved or how many times the character states have changed. One guiding
principle for finding a plausible evolutionary history is the principle of parsimony, which
states, in general, that the simplest answer is likely to be the correct one (also known as
Occam’s Razor). In the context of phylogenetics, trees with fewer character state transitions
are considered to be more reasonable than trees with a greater number of transitions. The
principle of parsimony asserts that the most parsimonious tree is our preferred hypothesis.
Thus, it is reasonable to assume that the tree with the lowest parsimony score (the fewest
character state changes) is the best estimate of the actual history of a group of species. But
remember, the tree is an estimate – the hypothesis with the most supporting evidence.
Additional data or a different analysis might change or further support one’s conclusion.

GLOSSARY
Reminder to check out this great resource for understanding phylogenetics: Evolutionary Trees – A Primer

ancestral: a character or character state present in the ancestor (i.e., taxon from which
other taxa descend).
character*: an observable feature, such as eye color or a behavior, or a specific locus (e.g.,
gene) in a sequence of DNA, such as cytochrome oxidase 1 (CO1). (Contrast with character
state.)
character matrix: an array that contains the character states (along the top) of a group of
taxa (along the left).
character state*: a specific form of a character; e.g., eye color is a character, whereas
brown eyes and blue eyes are character states. (Contrast with character.)
clade: a monophyletic group made up of an ancestor (node) and all of its descendants; also
called a “phylogenetic group.”
cladogram: tree-like representation of proposed relationships among taxonomic groups;
branch lengths do not represent time (i.e., absolute time axis absent). (Contrast with
phylogenetic tree.)
convergence: when organisms share similar character states but do not share them with
their most recent common ancestor, i.e., the character states evolved independently of one
another (example: the ability to fly in bats, birds, and insects).
derived: a new character or character state not present in the ancestor.
DNA alignment: An arrangement of sequences from a region (locus or gene) of DNA from
multiple organisms established for the purpose of comparing the states of homologous

Page 9 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

nucleic acid positions among taxa. Sequences are arranged based on similarities in the
order and identity of nucleic acids (As, Cs, Gs, and Ts) present in each sequence. Aligning
DNA sequences facilitates the construction of a character matrix from them, as illustrated
above in Figure 2.5..
fossil: Any preserved remnant or impression of an organism that lived in the past.
fossil record: all of the fossils that exist from the history of life, whether discovered or
undiscovered by people.
homolog*: one of two or more features (e.g., DNA sequence, structures, traits, or
properties) in different species that are similar due to descent from a common ancestor.
Homologs do not necessarily have the exact same structure, function, or behavior.
homology*: a similarity between two or more features that is inherited from a common
ancestor; such features are referred to as “homologous,” and each feature is called a
“homolog” of the other features.
homologous trait (See “homolog.”)
homoplasy: a character state of two or more taxa that was not inherited from a common
ancestor of those taxa; character states that arise independently in two or more lineages.
Homoplasies can result from evolutionary convergence, parallel evolution, or evolutionary
reversal.
ingroup*: in phylogenetics, the group of organisms of primary interest; evolutionary
relationships within the ingroup are determined using synapomorphies. (Contrast with
outgroup.)
locus (pl., loci)*: in genetics, a specific location on a chromosome.
monophyletic group (See “clade.”)
morphology: the study of the form and structure of organisms; also used as a noun to refer
to the form and structure of an organism or any of its parts (e.g., the morphology of an
insect’s forelimbs).
outgroup*: a group of organisms used as a point of reference for comparison with the
groups of primary interest; typically the most closely related taxon to, but not the ancestor
of, the set of taxa under study. Often displays plesiomorphic traits. (Contrast with ingroup.)
phylogenetic tree: tree-like representation of proposed relationships among taxonomic
groups; branch lengths do represent time (i.e., absolute time axis present). (Contrast with
cladogram.)
polarization: the process of indicating the directionality of character state changes from
ancestral to derived. Traditionally, ancestral states are coded as “0” and derived states are
coded with numbers greater than “0.”

Page 10 of 11
 Copyright © Fall2024, Dept. of Integrative Biology, UC Berkeley

reversal: the change in character state from a derived state to an ancestral state, such that
a descendent regains a characteristic of an ancestor. An example of the progression of
changes in a character history that shows reversal is (1) a change from an ancestral state to
a derived state and then (2) a change from a derived state back to the ancestral state. A
reversal can result in the incorrect inference of fewer evolutionary changes than actually
took place in a lineage.
sister taxa*: two phylogenetic groups (clades or taxa) that are each other’s closest
relatives.
synapomorphy: A derived or changed character state shared by two or more lineages in a
particular clade. Synapomorphies are indicators of common ancestry. For example, within
the clade of terrestrial vertebrates the ancestral character state is "has four legs." However,
both owls and parrots have the synapomorphic character state "has two legs and two
wings," indicating that owls and parrots are more closely related to each other than to four-
legged vertebrates.

* = denotes definitions modified from: Hillis, D. M., D. Sadava, H. C. Heller, and M. V. Price. 2012. Principles of
Life. Sinauer Associates, Inc. 909 pgs.

Page 11 of 11