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Chapter 26
Phylogeny and the Tree of Life
Node
Taxon A
Taxon B
Sister taxa
Taxon C
Taxon D
Taxon E
Most recent
common
ancestor
Polytomy
Taxon F
Systematics: classifying organisms and
determining their evolutionary relationships
Taxonomy
(classification)
Systematics
Phylogenetics
(evolutionary history)
Phylogeny: the evolutionary history of a
species or group of related species
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Tools used to determine evolutionary relationships:
1. Fossils
2. Morphology (homologous structures)
3. Molecular evidence (DNA, amino acids)
Who is more closely related?
Animals and fungi are more
closely related than either is
to plants.
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Taxonomy: science of classifying and naming
organisms
• Binomial nomenclature (Genus species)
• Naming system developed by
Carolus Linnaeus.
• Two key features remain
useful today:
▫ two-part names for
species
 Drosophila
melanogaster
 Caenorhabditis
elegans
▫ hierarchical classification
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REMEMBER!!
• Dear King Philip Came Over
For Good Spaghetti
• Dear King Philip Crossed
Over Five Great Seas
• Dear King Philip Came Over
From Germany Stoned
• Your own???
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Phylogenetic Tree
• Branching diagram that shows evolutionary history of
a group of organisms
• A phylogenetic tree represents a hypothesis about
evolutionary relationships
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
• A phylogenetic tree represents a hypothesis about
evolutionary relationships
• Each branch point represents the divergence of
two species
• Sister taxa are groups that share an immediate
common ancestor
• A rooted tree includes a branch to represent the
last common ancestor of all taxa in the tree
• A polytomy is a branch from which more than two
groups emerge
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Morphological and Molecular Homologies
• To infer phylogenies, systematists gather information
about morphologies, genes, and biochemistry of living
organisms
• Organisms with similar morphologies or DNA sequences
are likely to be more closely related than organisms with
different structures or sequences
– When constructing a phylogeny, systematists need to
distinguish whether a similarity is the result of
homology or analogy (review Ch 22)
• Homology = similarity due to shared ancestry
• Analogy = similarity due to convergent evolution
Cladogram: diagram that depicts patterns
of shared characteristics among taxa
• Clade = group of species that includes an ancestral
species + all descendents
• Shared derived characteristics are used to construct
cladograms
•
•
Shared ancestral character character that originated in an
ancestor of the taxon
Shared derived character evolutionary novelty unique to a
particular clade
Turtle
Cladogram
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Lancelet (outgroup)
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Leopard
Hinged jaws
Vertebral column
Constructing a phylogenetic tree
A 0 indicates a character is absent; a 1
indicates that a character is present.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
• An outgroup is a species or group of species
that is closely related to the ingroup, the various
species being studied
• Systematists compare each ingroup species with
the outgroup to differentiate between shared
derived and shared ancestral characteristics
– Homologies shared by the outgroup and
ingroup are ancestral characters that predate
the divergence of both groups from a
common ancestor
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Phylogenetic Trees with Proportional Branch
Lengths
• In some trees, the length of a branch can
reflect the number of genetic changes that
have taken place in a particular DNA sequence
in that lineage
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
• In other trees, branch length can represent
chronological time, and branching points can
be determined from the fossil record
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Mouse
PALEOZOIC
542
MESOZOIC
251
Millions of years ago
CENOZOIC
65.5
Present
Draw a phylogenetic tree based on the data below. Draw hatch
marks on the tree to indicate the origin(s) of each of the 6
characters.
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Answer:
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Maximum Parsimony and Maximum Likelihood
• Systematists can never be sure of finding the
best tree in a large data set
– 50 species comparison = 3 x 1076 trees
• They narrow possibilities by applying the
principles of maximum parsimony and
maximum likelihood
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
• Maximum parsimony assumes that the tree
that requires 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
Fig. 26-14
Human
Mushroom
Tulip
0
30%
40%
0
40%
Human
Mushroom
0
Tulip
(a) Percentage differences between sequences
15%
5%
5%
15%
15%
10%
20%
25%
Tree 1: More likely
Tree 2: Less likely
(b) Comparison of possible trees
Fig. 26-15-1
Species I
Species III
Species II
Three phylogenetic hypotheses:
I
I
III
II
III
II
III
II
I
Fig. 26-15-4
Site
1
2
3
4
Species I
C
T
A
T
Species II
C
T
T
C
Species III
A
G
A
C
Ancestral
sequence
A
G
T
T
1/C
I
1/C
II
I
III
III
II
1/C
II
III
I
1/C
3/A
2/T
I
2/T
3/A
3/A 4/C
3/A
4/C
III
II
2/T
4/C
II
III
6 events
I
III
II
4/C
1/C
I
2/T 3/A
2/T 4/C
I
I
III
II
III
II
III
II
I
7 events
7 events
• The best hypotheses for phylogenetic trees fit the
most data: morphological, molecular, and fossil
• Phylogenetic bracketing allows us to predict
features of an ancestor from features of its
descendants
Common
ancestor of
crocodilians,
dinosaurs,
and birds
Fig. 26-17
Front limb
Hind limb
Eggs
(a) Fossil remains of Oviraptor
and eggs
(b) Artist’s reconstruction of the dinosaur’s posture
Concept 26.4: An organism’s evolutionary history
is documented in its genome
• Comparing nucleic acids or other molecules to
infer relatedness is a valuable tool for tracing
organisms’ evolutionary history
• DNA that codes for rRNA changes relatively
slowly and is useful for investigating branching
points hundreds of millions of years ago
• mtDNA evolves rapidly and can be used to
explore recent evolutionary events
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Gene Duplications and Gene Families
• Gene duplication increases the # of genes in
genome, more opportunities for evolutionary
changes
• Like homologous genes, duplicated genes can be
traced to a common ancestor
– Orthologous genes- single copy in the genome,
homologous between species; can diverge only
after speciation occurs
– Paralogous genes- gene duplication, found in
more than one copy in the genome; can diverge
within the clade that carries them and often evolve
new functions
Fig. 26-18
Ancestral gene
Ancestral species
Speciation with
divergence of gene
Species A
Orthologous genes
Species B
(a) Orthologous genes
Species A
Gene duplication and divergence
Paralogous genes
Species A after many generations
(b) Paralogous genes
Genome Evolution
• Orthologous genes are widespread and extend
across many widely varied species
– Highly conserved
• Gene number and the complexity of an
organism are not strongly linked
• Genes in complex organisms appear to be very
versatile and each gene can perform many
functions
– Alternative splicing, gene regulation
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Molecular Clocks
• To extend molecular phylogenies beyond the fossil record,
we must make an assumption about how change occurs
over time
• A molecular clock uses constant rates of evolution in
some genes to estimate the absolute time of evolutionary
change
• In orthologous genes, nucleotide substitutions are
proportional to the time since they last shared a common
ancestor
• In paralogous genes, nucleotide substitutions are
proportional to the time since the genes became
duplicated
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• Molecular clocks are calibrated against
branches whose dates are known from the
fossil record
90
60
30
0
0
30
60
90
Divergence time (millions of years)
120
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
• The three-domain system is supported by data
from many sequenced genomes
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Fig. 26-21
EUKARYA
Dinoflagellates
Forams
Ciliates Diatoms
Red algae
Land plants
Green algae
Cellular slime molds
Amoebas
Euglena
Trypanosomes
Leishmania
Animals
Fungi
Sulfolobus
Green nonsulfur bacteria
Thermophiles
Halophiles
(Mitochondrion)
COMMON
ANCESTOR
OF ALL
LIFE
Methanobacterium
ARCHAEA
Spirochetes
Chlamydia
Green
sulfur bacteria
BACTERIA
Cyanobacteria
(Plastids, including
chloroplasts)
A Simple Tree of All Life
• The tree of life suggests that eukaryotes and
archaea are more closely related to each other
than to bacteria
• The tree of life is based largely on rRNA genes,
as these have evolved slowly
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• There have been substantial interchanges of
genes between organisms in different domains
• Horizontal gene transfer is the movement of
genes from one genome to another
• Horizontal gene transfer complicates efforts to
build a tree of life
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-22
Bacteria
Eukarya
Archaea
4
3
2
Billions of years ago
1
0
Is the Tree of Life Really a Ring?
• Some researchers suggest that eukaryotes
arose as an endosymbiosis between a
bacterium and archaean
• If so, early evolutionary relationships might be
better depicted by a ring of life instead of a tree
of life
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
You should now be able to:
1. Explain the following terms: taxonomy, taxa/taxon, phylogeny,
binomial nomenclature
2. Why are some phlyogenetic trees better than others?
3. What is meant by the statement: “a phylogenetic tree is a
hypothesis”
4. Distinguish between the following terms: shared ancestral and
shared derived characters; orthologous and paralogous
genes; homology and analogy
4. Explain molecular clocks and discuss their limitations
5. What is our current classification systems like? What
concepts have we maintained from Linnaean classification?