Chapter 26

Phylogeny and the Tree of Life

• Biologists estimate that there are about 5 to 100 million
species of organisms living on Earth today.

• Evidence from morphological, biochemical, and gene

sequence data suggests that all organisms on Earth are
genetically related, and the genealogical relationships of living
things can be represented by a vast evolutionary tree,
the Tree of Life.
• The Tree of Life then represents the phylogeny of organisms,
the history of organismal lineages as they change through
time.
– In other words, phylogeny is the evolutionary history of
a species or group of related species.
• Phylogeny assumes that all life arise from a previous
ancestors and that all organisms (bacteria, fungi, protist,
plants, animals) are connected by the passage of genes
along the branches of the phylogenetic tree.
• The discipline of systematics classifies organisms and
determines their evolutionary relationships.
• Systematists use fossil, molecular, and genetic data to infer
evolutionary relationships.
• Hence, systematists depict evolutionary relationships among
organisms as branching phylogenetic trees.
• A phylogenetic tree represents a hypothesis about
evolutionary relationships.
• Taxonomy is the science of organizing, classifying and
naming organisms.

• Carolus Linnaeus was the scientist who came up with the

two-part naming system (binomial system).
– The first part of the name is the genus
– The second part, called the specific epithet, is the species
within the genus.
– The first letter of the genus is capitalized, and the entire
species name is italicized.
• Homo sapiens or H. sapiens
• All life are organize into the following taxonomic groups:
domain, kingdom, phylum, class, order, family, genus,
and species. (Darn Kids Playing Chess On Freeway
Gets Squished).

• The higher the taxonomic group, the more inclusive it is and

the lower the taxonomic group, the less inclusive it is.

• For example, the Domain Eukarya contains all organisms

that have eukaryotic cells. This is very inclusive.

• On the other hand, the genera Homo contains only modern

humans and close relatives. This is very exclusive.
Figure 26.3

Species:
Panthera pardus
Genus:
Panthera
Family:
Felidae
Order:
Carnivora

Class:
Mammalia

Phylum:
Chordata

Domain: Kingdom:
Bacteria Animalia Domain:
Archaea
Domain:
Eukarya
Understanding Phylogenetic Tree
• Each branch point of the phylogenetic tree represents the
divergence (separation) of two or more species.

• A rooted tree includes a branch to represent the last common

ancestor of all taxa (group) in the tree.
• Sister taxa are groups that share an immediate common
ancestor. In the phylogenetic tree below, domestic dog and
wolf are sister taxon as they share the common ancestor
Canis. Are there any other sister taxa?
• Note, a taxon or taxa (plural) is a taxonomic unit (group of
related organisms) at any level of hierarchy. It could occur at
the Kingdom level and all the way to the species level.

• For example, Panthera, Felidae, Carnivora, Canis, Lutra,

Mephitis are taxa.
• A basal taxon is a taxon that diverges early in the history of
that group. A basal taxon typically originates near the
common ancestor of the group.

• For example, in the next slide (fig. 26.5), Taxon G represents

a basal taxon because 1) it diverged early in time and 2) it
diverge near the time of the ancestral taxon.

• A polytomy is a branch from which more than two groups or

taxons emerged, forming a pitchfork shape.

• Polytomy represents an unknown cause of the divergence.

(See figure 26.5). For example, we do not have a clear
knowledge of why Taxa D, E, and F diverged from their
common ancestor.
Figure 26.5

Branch point:
where lineages diverge Taxon A

Taxon B
Sister
taxa
Taxon C

Taxon D

Taxon E
ANCESTRAL
LINEAGE
Taxon F
Basal
Taxon G taxon
This branch point This branch point forms a
represents the polytomy: an unresolved
common ancestor of pattern of divergence.
taxa A–G.
What We Can and Cannot Learn from
Phylogenetic Trees
• 1. Phylogenetic trees show patterns of descent, not
phenotypic similarity.

• 2. Phylogenetic trees do not indicate when species evolved or

how much change occurred in a lineage.

• 3. It should not be assumed that a taxon evolved from the

taxon next to it.
 Phylogenies Are Inferred From
Morphological and Molecular Data
• In order to infer phylogenies or determine how groups of
organisms are related by evolution, systematists gather
information about morphologies, genes, and biochemistry of
the organisms.

• Organisms with similar morphologies or molecular sequences

are likely to be more closely related than organisms with
different structures or sequences. We referred to these
phenotypic and molecular similarities shared by group of
organisms as homologies and homologies indicate a shared or
common ancestry.

• For example, we believe chimps to be our closest living

ancestor because we posses similar anatomical structures i.e.
skull bones and similar DNA sequence i.e. DNA. (see next
slides)
Molecular Homology
Morphological Homology
Sorting Homology from Analogy
• When constructing a phylogeny, systematists need to
distinguish whether similarities among organisms is the result
of homology or analogy.
– Homology is similarity due to shared ancestry
– Analogy is similarity due to convergent evolution

• If we look at the bones that make up the appendages of

humans, cats, whales, and bats, we will find that these bones
are quite morphologically similar. It can be said that the
appendages of these animals are homologous and it further
suggests that these animals share a common ancestor.
• Now if we were to examine the wings of insects and birds, we
will find that they are not morphologically similar even though
they serve the same function of flight.

• The wings of birds and insects then are analogous

structures. Analogous structures evolved in unrelated
organisms due to convergent evolution, not because they
share a common ancestor.

• Convergent evolution occurs when unrelated organisms

live in similar environment and faces similar pressures. This
forces these unrelated organisms to evolve similar
adaptations such as flippers of dolphins and fins of fishes.
• Another example of analogous structures is seen in the tails
of whales and fish. These unrelated groups shared an
analogous structure (tail) due to both facing the same
environmental pressure i.e. an aquatic environment.

• In general, the more complex two similar structures are, the

more likely it is that they are homologous.

• Once homologous characters have been identified, they can

be used to infer a phylogeny.
• When taxonomist and systematist classify organisms, they
can organized these organisms into groups by looking only at
the common characteristics shared by these groups OR by
how these organisms are evolutionarily related.

• So if the focus is primarily on shared traits, then this

approach is referred to as phenetic.

• If the focus is primarily based on evolutionary relationships

and shared characteristics, then it is referred to as cladistic.

• The basic objective of cladistics is to provide a scheme

(cladogram) showing the most likely evolutionary pathway for
a given group or species based on the characters that it
shares with its relatives.
• Simply put….Cladistics is one approach to phylogeny.

• A clade is a group of species that includes an ancestral

species and all of its descendants. Often this type of clade
that includes only an ancestral species and all its descents is
described as being monophyletic.
• On the other hand, a clade is described to be paraphyletic if
it consists of an ancestral species and some, but not all, of
the descendants.
• And a clade is said to be polyphyletic if it consists of various
species with different ancestors.
Figure 26.10

(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group

A A A

B Group  B B
Group 
C C C

D D D

E E Group  E

F F F

G G G
 Shared Ancestral and
Shared Derived Characters
• In comparison with its ancestor, an organism has both shared
and different characteristics.

• A shared ancestral character is a character that originated

in an ancestor of that taxon or group. (see next slide)

• A shared derived character is an evolutionary new trait

unique to that particular clade or group. (see next slide)
• Four legs is a shared ancestral character found in frog,
crocodile, platypus, kangaroo and elephant.

• Mammary glands is a shared derived character found in

platypus, kangaroo, and elephant.
• When inferring evolutionary relationships, it is useful to know
in which clade a shared derived character first appeared.

• In a cladogram, there is an ingroup and an outgroup.

• The ingroup is comprise of taxa which are hypothesized to

be more closely related to each other than to any other. The
outgroup is a group that has diverged before the ingroup.
The outgroup is used as a point of comparison for the
ingroup.
• Systematists compare each ingroup species with the
outgroup to differentiate between shared derived and shared
ancestral characteristics.

• Characters shared by the outgroup and ingroup are ancestral

characters that predate the divergence of both groups from a
common ancestor.

• In the following diagram, if leopard and domestic cat are

designated as an ingroup, then wolf, horse, and turtle are
considered an outgroup.
• The length of a cladogram or phylogenetic tree branch can
represent either:
– The number of genetic changes that have taken place in a
particular DNA sequence OR
– Chronological time in the evolution of certain clades
• Systematists can never be sure of constructing the best tree
in a large data set.

• To identify the most likely phylogenetic tree, systematists

apply the principles of maximum parsimony and
maximum likelihood.

• The principles of maximum parsimony says that the tree

with the fewest evolutionary events (appearances of shared
derived characters) is the most likely.

• The principle of maximum likelihood states that, given

certain rules about how DNA changes over time, a tree can
be found that reflects the most likely sequence of
evolutionary events. Computer programs are used to search
for trees that are parsimonious and likely.
• Given the option of the two tree below, “a” is the better tree
according to the rule of maximum parsimony because it has
the least evolutionary changes and is the simplest.
Molecular Clocks
• Another tool use by systematists to construct a phylogenetic
tree is a molecular clock. Molecular clocks help
systematists find out how many years ago two or more
groups or taxa diverged from a common ancestor.

• For example, let’s say that two groups diverged from a

common ancestor. If we know the length of time it takes for a
shared gene to mutate, we can trace the gene back to the
common ancestor and estimated how long ago these groups
diverged.
Molecular Clock
From Two Kingdoms to
Three Domains
• Early taxonomists classified all species as either plants or
animals.

• Later, five kingdoms were recognized: Monera (prokaryotes),

Protista, Plantae, Fungi, and Animalia.

• More recently, the three-domain system has been adopted:

Bacteria, Archaea, and Eukarya.
Figure 26.21

Eukarya
Land plants Dinoflagellates
Green algae Forams
Ciliates Diatoms
Red algae

Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Fungi

Sulfolobus Green
nonsulfur bacteria
Thermophiles (Mitochondrion)

Spirochetes
Halophiles Chlamydia
COMMON
ANCESTOR Green
OF ALL sulfur bacteria
LIFE
Methanobacterium Bacteria
Cyanobacteria
Archaea (Plastids, including
chloroplasts)
The End