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Chapter 26
Phylogeny and the Tree of Life
PowerPoint® Lecture Presentations for
Biology
Eighth Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Overview: Investigating the Tree of Life
• Phylogeny - evolutionary history of a species
or group of related species
• Systematics - classifies organisms and
determines their evolutionary relationships
based on fossil, molecular, and genetic data
• Taxonomy - ordered division and naming of
organisms
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Binomial Nomenclature
• Carolus Linnaeus - system of taxonomy based on
resemblances
– 1.Two-part scientific name of a species is called a
binomial
• The first part of the name is the genus. The second
part, called the specific epithet, is unique for each
species within the genus
• The first letter of the genus is capitalized, and the
entire species name is italicized. Both parts
together name the species.
– 2. Hierarchical classification
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Fig. 26-3
Species:
Panthera
pardus
Genus: Panthera
A
taxonomic
unit at any
level of
hierarchy
is called a
taxon
Family: Felidae
Order: Carnivora
Class: Mammalia
Phylum: Chordata
Kingdom: Animalia
Bacteria
Domain: Eukarya
Archaea
Linking Classification and Phylogeny
• Systematists depict evolutionary relationships in branching
phylogenetic trees (hypothesis)
• Systematists have proposed the PhyloCode, which
recognizes only groups that include a common ancestor
and all its descendents
• 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
• Polytomy - branch where more than two groups emerge
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-5
Branch point
(node)
Taxon A
Taxon B
Taxon C
ANCESTRAL
LINEAGE
Taxon D
Taxon E
Taxon F
Common ancestor of
taxa A–F
Polytomy
Sister
taxa
What We Can and Cannot Learn from
Phylogenetic Trees
• Phylogenetic trees DO show patterns of
descent. They DO NOT indicate when species
evolved or how much genetic change occurred
in a lineage.
• It shouldn’t be assumed that a taxon evolved
from the taxon next to it
• Phylogeny provides important information
about similar characteristics in closely related
species.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-UN1
(a)
A
B
D
B
D
C
C
C
B
D
A
A
(b)
(c)
Concept 26.2: Phylogenies are inferred from
morphological and molecular data
• Homology - similarity due to shared ancestry
• Analogy - similarity due to convergent evolution
• Convergent evolution - similar environmental pressures and natural
selection produce similar (analogous) adaptations in organisms from
different evolutionary lineages
• Bat and bird wings are homologous as forelimbs, but analogous as
functional wings
• Analogous structures or molecular sequences that evolved
independently are also called homoplasies
• Homology can be distinguished from analogy by comparing fossil
evidence and the degree of complexity
• The more complex two similar structures are, the more likely it is that
they are homologous
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Concept 26.3: Shared characters are used to
construct phylogenetic trees
• Molecular systematics uses DNA and other
molecular data to determine evolutionary
relationships
• Cladistics groups organisms by common
descent
• Clade - group of species that includes an
ancestral species and all its descendants
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•Monophyletic - consists of the ancestor species and all its descendants
(valid)
•Paraphyletic - consists of an ancestral species and some, but not all,
of the descendants
•Polyphyletic - consists of various species that lack a common ancestor
A
A
A
B
B
C
C
C
D
D
D
E
E
F
F
F
G
G
G
B
Group I
(a) Monophyletic group (clade)
Group II
(b) Paraphyletic group
E
Group III
(c) Polyphyletic group
Shared Ancestral and Shared Derived Characters
• In comparison with its ancestor, an organism
has both shared and different characteristics
• Shared ancestral character - character that
originated in an ancestor of the taxon
• Shared derived character - evolutionary
novelty unique to a particular clade
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Inferring Phylogenies Using Derived Characters
• Outgroup - species or group of species that is closely
related to the ingroup (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
Fig. 26-11
TAXA
Tuna
Leopard
Lancelet
(outgroup)
Vertebral column
(backbone)
0
1
1
1
1
1
Hinged jaws
0
0
1
1
1
1
Lamprey
Tuna
Vertebral
column
Salamander
Hinged jaws
Four walking legs
0
0
0
1
1
1
Turtle
Four walking legs
Amniotic (shelled) egg
0
0
0
0
1
1
Hair
0
0
0
0
0
1
Amniotic egg
(a) Character table
Leopard
Hair
(b) Phylogenetic tree
Fig. 26-12
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
Maximum Parsimony and Maximum Likelihood
• Systematists can never be sure of finding the best tree
in a large data set. They narrow possibilities by
applying the principles of maximum parsimony and
maximum likelihood
• 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
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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
Phylogenetic Trees as Hypotheses
• 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
descendents
• This has been applied to infer features of
dinosaurs from their descendents: birds and
crocodiles
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Fig. 26-16
Lizards
and snakes
Crocodilians
Common
ancestor of
crocodilians,
dinosaurs,
and birds
Ornithischian
dinosaurs
Saurischian
dinosaurs
Birds
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 number of genes in the
genome, providing more opportunities for evolutionary changes
• Like homologous genes, duplicated genes can be traced to a
common ancestor
• Orthologous genes - found in a single copy in the genome
and are homologous between species
– They can diverge only after speciation occurs
• Paralogous genes result from gene duplication, so are found
in more than one copy in the genome
– They can diverge within the clade that carries them and
often evolve new functions
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
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
• 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
• To extend molecular phylogenies beyond the
fossil record, we must make an assumption
about how change occurs over time
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Molecular Clocks
• 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
• Molecular clocks are calibrated against branches
whose dates are known from the fossil record
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Neutral Theory
• Neutral theory states that much evolutionary
change in genes and proteins has no effect on
fitness and therefore is not influenced by
Darwinian selection
– It states that the rate of molecular change in
these genes and proteins should be regular
like a clock
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Difficulties with Molecular Clocks
• The molecular clock does not run as smoothly as
neutral theory predicts
• Irregularities result from natural selection in which
some DNA changes are favored over others
• Estimates of evolutionary divergences older than
the fossil record have a high degree of uncertainty
• The use of multiple genes may improve estimates
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
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
• Horizontal gene transfer - movement of
genes from one genome to another
– complicates efforts to build a tree of life
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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
Eukarya
of life
Bacteria
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Archaea