Biology 11E
Name: _____________
Chapter 26 Phylogeny and the Tree of Life
AP Biology links:
Big Idea 1: The process of evolution drives the diversity and unity of life.
1b2 Phylogenetic trees and cladograms are graphical representations (models) of evolutionary
history that can be tested. Chapters 26.1, 26.2, 26.3
1d2 Scientific evidence from many different disciplines supports models of the origin of life.
Chapter 26.6
Here is a legless lizard:
How did scientists decide that this is actually a legless lizard, and NOT a snake? Page 536
_____________________________________________________________________________________
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_____________________________________________________________________________________
Questions like the above are part of the study of phylogeny. What is phylogeny? __________________
_____________________________________________________________________________________
Constructing phylogenies is part of systematics. What is systematics? ____________________________
_____________________________________________________________________________________
What types of evidence are used to construct phylogenies? ____________________________________
_____________________________________________________________________________________
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DNA evidence has been used to clarify the following evolutionary
relationships between animals, fungi and plants
Without
this type of evidence, most people would think that fungi are more
closely related to ____________________ than they are to humans.
Choose any organism, animal or plant and research why it has been grouped with others of the same
family as it. (you will report back next class)
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Concept 26.1 Phylogenies show evolutionary relationships
Start by viewing the Activity: Classification Schemes under Concept 26.1 on the website.
In studying phylogenies, we will first look at how organisms are named and classified. The naming and
classifying of organisms is called ______________________.
Organisms are named using the __________________ system first introduced by
____________________________________.
In the example at the right, the panther is
called Panthera pardus. The first part of the
name is the ___________ that the organism
belongs in. The second part of the name, the
species epithet, represents the
___________________ of the organism
within that genus. The first letter of the genus
name is _______________________ and the
whole name is written in
___________________.
Linnaeus also introduced the hierarchical
system of classification where each taxonomic
level is increasingly inclusive .

In this system, what is a taxon?
___The named taxonomic unit at any level.
(taxa = pleural)
Carnivora is a taxon at the order level. _
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How closely related are domesticed cats to panthers?
Phylogenetic trees are used to show the evolutionary history of a group of organisms. For example, this
phylogenetic tree shows evolutionary relationships between some carnivores:

Evolutionary relationships are often represented as a series of dichotomies, or two-way branch
points.
o Each branch point represents the divergence of two evolutionary lineages from a common
ancestor.
This diagram, show the relationship between classification and phylogeny.
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What does each of the branch points of a phylogenetic tree represent? _
This tree traces possible evolutionary relationships between some of the taxa within order carnivora. The
most common ancestry between species is illustrated here. _________________
The following generalized diagram shows some characteristics of a typical phylogenetic tree:
On the phylogenetic tree
above, use a ‘1’ to indicate the
common ancestor of Taxa A,
B, and C.
Put a ‘2’ at the common
ancestor of Taxa B and C. Why are B and C called ‘sister taxa’?
Sister taxa are groups of organisms that share an immediate common ancestor and are each
other’s closest relatives.
Why do we say that this tree is ‘rooted’? __
A rooted tree includes the most recent common ancestor to all taxa in the tree.
What is a ‘polytomy’?
An unresolved pattern of divergence where more than two descendent groups emerge.
The term basal taxon refers to a lineage that diverges early in the history of a group, lying on
a branch that originates near the common ancestor of the group.

Three key points about phylogenetic trees should be emphasized.
1. Phylogenetic trees are intended to show patterns of descent, not phenotypic similarity.
Closely related organisms may resemble one another due to common ancestry, but may
not if their lineages have evolved at different rates or faced very different environmental
conditions.
2. The sequence of branching in a tree reflects patterns of descent and does not indicate the
absolute ages of particular species.
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3. A taxon in a phylogenetic tree did not evolve from an adjacent taxon. Rather, both taxa
evolved from a common ancestor.

A species’ phylogeny can provide useful information.
o From a phylogeny of corn based on DNA data, researchers have identified two closely
related species of wild grasses that may serve as “reservoirs” of beneficial alleles. These
alleles may be transferred to cultivated corn by plant breeding or genetic engineering.
o Phylogenetic trees played a role in demonstrating that “whale meat” sold in Japan was
illegally harvested from protected species.
Here is a practical application of a phylogenetic tree. This, in particular, is a gene tree: (see pp
539-540) Inquiry on page 539 What is the
species of food being sold as whale meat?
Read about the situation and answer these
questions:
Where did the unknown samples come from?
___Fish markets in Japan____
What evidence was used to construct the
phylogenetic tree? __A section of mitochondria DNA was sequenced and compared to the
mitochondrial DNA of known whale species.
Which of the unknown samples were actually found to be illegal whale meat? _
Minke, humpback and fin whale.
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Do Concept Check 26.1 on p 540.
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Concept 26.2 Phylogenies are inferred from morphological and molecular data
In constructing phylogenies, why is it important to look at homologous structures and
homologous molecular sequences, such as are found in DNA?
____________________________________________
______________________________________________________________________________
Which homologies are more useful in determining phylogenies, morphological homologies,
or molecular homologies and why?
Organisms that share similar morphologies or DNA sequences are likely to be more closely
related than organisms without such similarities.
The moles pictured at the right seem to share many common morphological features. We say
these structures are analogous because they have evolved as a result of similarities in the
organisms’ __environment/habitat__ and not because they share a close common ancestor
Australian mole on top and North
American mole on bottom.
These organisms are similar because
they have undergone
convergent
evolution as opposed to
divergent evolution. It is important to
separate phenotype from genotype when
constructing phylogenetic trees.
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With respect to DNA, if genes in two different organisms share many portions of their
nucleotides, then we say the genes are _________________________________. The more
similar the genes ________________________________________________________. This
diagram shows how computer programs can be used to find and align homologous regions that
would not be obvious to a casual observer:
o
If the genes in two organisms have very
similar nucleotide sequences, it is
highly likely that the genes are
homologous.

It may be difficult to carry out molecular
comparisons of nucleic acids.

The first step in molecular comparisons is
to align nucleic acid sequences from the
two species being studied.
o In closely related species, sequences
may differ at only one or a few sites.
o Distantly related species may have
many differences or sequences of
different length.
As with morphological characters, it is
necessary to distinguish homology from
analogy to determine the usefulness of
molecular similarities for reconstruction of
phylogenies.
o
Very similar sequences are most likely
homologies.
o In distantly related organisms, identical
bases in otherwise different sequences
may simply be coincidental matches or molecular homoplasies.
Computer programs can also indicate whether matching DNA bases are simply coincidental (a
molecular homoplasy) or actually
homologous. The example at the right
has been determined to be a molecular
homoplasy rather than a homologous
sequence indicative of a common ancestor. The discipline that analyzes molecular data such as
this to determine phylogenetic relationships is called ___molecular_____ systematics.
Do Concept Check 26.2
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Concept 26.3 Shared characters are used to construct phylogenetic trees
In cladistics, scientists put species into groups called ___________________, which include the
common ancestor of all the species in the clade. The goal in this type of systematics is to create
___________________ groups or clades, because these groups show the
__________________________ relationship between the species. If species are placed in
_____________________________ or _________related_________ groups, the correct
evolutionary relationship is not shown by the groupings.
To identify clades, biologists identify shared ancestral characters and shared derived
characters.
A shared ancestral character is one that originated in an __ancestor____ of the clade, such as the
vertebral column of mammals.
A shared derived character is one that is an evolutionary novelty unique to a particular clade, such
as hair in all mammals. Hair uniquely identifies the clade of mammals from other vertebrates.

The presence of a backbone can qualify as a shared derived character, but at a deeper branch
point that distinguishes all vertebrates from other mammals.
o Among vertebrates, the backbone is a shared ancestral character because it evolved in the
ancestor common to all vertebrates.
In a character table, a _0__ indicates that the
character is absent in a group, and a __1_
indicates that the character is present.
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Character tables can be used to construct possible phylogenetic trees. This example shows how a
phylogenetic tree for vertebrates could be constructed:
The group that diverged before the group we are studying is used for comparison, and is called
the ___________________________. In the above example, this group is represented by the
___________________________, which does not have a backbone, but is similar to vertebrates
in many ways.
Relative amounts of genetic change can be seen in the following phylogenetic tree by comparing
the total horizontal line from the common ancestor. Which organism has undergone the most
genetic change in this lineage? ____________________________________ The least? __
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In this phylogenetic tree, we see that all the organisms have been evolving for the same amount of
time, but we can also see how long ago each group diverged from the others:
How long ago did the mouse line diverge from the human line?
___________________________. The amphibian group from the chicken/human/mouse group?
____________________________
In constructing phylogenetic trees, scientists use two principles:
Maximum parsimony: __the fewest base changes between an organism and its ancestor and
therefore the fewest evolutionary differences. __
Maximum likelihood: ___the most likely sequence of evolutionary events. ___
Phylogenetic trees are hypotheses.

Any phylogenetic tree represents a hypothesis about how the organisms in the tree are related.
o The best hypothesis is the one that best fits all the available data.
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We can use phylogenetic trees to predict characteristics of fossil organisms, such as dinosaurs.
Which modern group of organisms would be most similar to dinosaurs?
o
o
o
o
o
o
Evidence suggests that birds descended from a group of bipedal Saurischian theropod
dinosaurs.
The closest living relatives of birds are crocodiles.
Birds and crocodiles share a number of features: Both have four-chambered hearts. Both
“sing” to defend territories and attract mates. Both brood their eggs, birds by sitting on
them and crocodiles by covering their eggs with their neck.
Based on these observations, biologists predict that dinosaurs had four-chambered hearts,
sang, and brooded eggs in nests.
The fossil record does not provide evidence of dinosaur heart structure or singing
behavior. However, fossilized dinosaur nests have been found with fossilized adults
crouched over the eggs in a brooding posture.
This evidence provides independent data supporting the hypothesis that birds descended
from dinosaurs.
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Here is fossil evidence that
supports the prediction that
dinosaurs have nests and brood
their eggs:
Concept 26.4 An organism’s evolutionary history is documented in its genome
Why is the DNA that codes for rRNA useful in studying relationships between taxa that diverged
hundreds of millions of years ago? The DNA that codes for ribosomal RNA (rRNA) changes
relatively slowly, so DNA sequences in these genes can be compared to sort out relationships
between taxa that diverged hundreds of millions of years ago.
o
Studies of rRNA sequences indicate that fungi are more closely related to animals than to
plants.
o
In contrast, mitochondrial DNA (mtDNA) evolved relatively recently and can be used
to explore recent evolutionary events, such as relationships between groups within a species.
o
One research team has used mtDNA to trace the relationships between Native
American groups.
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Concept 26.5 Molecular clocks help track evolutionary time
Because the rate of mutation in specific genes tends to remain constant, we can use the number of
mutations as an indication of how long ago two species diverged and how long ago gene
duplication occurred. This means we have a molecular clock to measure evolutionary time. The
following mammalian molecular clock was constructed using the code for seven different
proteins: Refer to figure 26.19 on page 550
If two mammals show 40 nucleotide differences in these particular protein codes, approximately
how long ago did the species diverge from each other? __________________________
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Here is a molecular clock constructed from a gene in HIV. By projecting backwards, when did
the first AIDS virus emerge into the human population? ________________________
Refer to fig. 26.20 on page 551
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26.6 New information continues to revise our understanding of the tree of life.
Molecular systematics has allowed scientists to refine their understanding of how modern day
organisms should be classified. As a result, we have moved from a two kingdom system:
to a five-kingdom system:
to the modern three-domain system:
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Evidence from the analysis of the DNA that codes for rRNA has allowed scientists to construct
the following possible tree of life.
Note that only the three branches shown in red above represent multicellular organisms. Most of
the history of life has been dominated by single-celled organisms.
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This simplified tree of life indicates that there has been exchange of genes between the three
domains (indicated by the white arrows) at various times in the history life.
Evidence suggests that there have been many such horizontal gene transfers.
1. Next to each picture below, name and briefly describe the domain that it represents.
I
_________________________________________________________________
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_________________________________________________________________
____________________________________________________
II
___________________________
III
________________________________________________________________________
________________________________________________________________________
__________________________________________
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__________________________________________
________________________________________________________________________
________________________________________________
http://www.youtube.com/watch?v=BQ1JaYxBH40&feature=fvw classification on you tube.
2. Use the table to briefly explain how the kingdoms of Domain Eukarya are divided.
Kingdom
Uni or
Type of nutrition
multicellular
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Other relevant information
Multiple kingdoms
Kingdom
Uni or
Type of nutrition
multicellular
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Other relevant information
Past exam question (2011)
Explain THREE methods that have been used to investigate the phylogeny of organisms.
Describe a strength or weakness of each method.
Methods (1 point)
Fossils (paleontology)
Anatomy/morphology
Embryology/development
Molecular traits (amino acid
sequence in proteins or base
sequence in DNA)
Behavioral traits
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AND Strengths (1 point)
Determine time; reveal extinct
species.
Homologous structures indicate
evolutionary relationships.
Reveals similarities in structures
and patterns of development that
are not evident in adults.
Large numbers of traits. Allow
study of evolution between
closely related species. Most
accurate.
Some behaviors are genetic (e.g.,
frog calls).
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OR Weaknesses (1 point)
Not all species leave fossils.
Fossil record is incomplete.
Analogous structures. Some taxa
have little diversity (e.g.,
bacteria). Some morphology
reflects environment or diet.
Similarities between species may
be lost in later development.
No (or little) data for extinct
species. Variation within species
blurs differences between species.
Behavior maybe culturally
transmitted or learned (e.g., bird
calls).