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Chapter 25
Phylogeny and Systematics
PowerPoint Lectures for
Biology, Seventh Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Overview: Investigating the Tree of Life
• Phylogeny is the evolutionary history of a species
or group of related species
• Biologists draw on the fossil record, which
provides information about ancient organisms
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Systematics is an analytical approach to
understanding the diversity and relationships of
organisms, both present-day and extinct
• Systematists use morphological, biochemical, and
molecular comparisons to infer evolutionary
relationships
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Concept 25.1: Phylogenies are based on common ancestries
inferred from fossil, morphological, and molecular evidence
• To infer phylogenies, systematists gather
information about morphologies, development,
and biochemistry of living organisms
• They also examine fossils to help establish
relationships between living organisms
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The Fossil Record
• Sedimentary rocks are the richest source of fossils
• Sedimentary rocks are deposited into layers called
strata
Video: Grand Canyon
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-3
Rivers carry sediment to the
ocean. Sedimentary rock layers
containing fossils form on the
ocean floor.
Over time, new strata are
deposited, containing fossils
from each time period.
As sea levels change and the
seafloor is pushed upward,
sedimentary rocks are exposed.
Erosion reveals strata and fossils.
Younger stratum
with more recent
fossils
Older stratum with
older fossils
• The fossil record is based on the sequence in
which fossils have accumulated in such strata
• Fossils reveal ancestral characteristics that may
have been lost over time
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• Though sedimentary fossils are the most common,
paleontologists study a wide variety of fossils
Animation: The Geologic Record
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-4
Leaf fossil, about 40 million
years ago
Petrified trees in Arizona, about 190
million years old
Insects preserved whole in amber
Dinosaur bones being
excavated from sandstone
Casts of ammonites, about
375 million years old
Boy standing in a 150-million-year-old
dinosaur track in Colorado
Tusks of a 23,000-year-old mammoth, frozen whole
in Siberian ice
Morphological and Molecular Homologies
• In addition to fossils, phylogenetic history can be
inferred from morphological and molecular
similarities in living organisms
• Organisms with very similar morphologies or
similar DNA sequences are likely to be more
closely related than organisms with vastly different
structures or sequences
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Sorting Homology from Analogy
• In constructing a phylogeny, systematists need to
distinguish whether a similarity is the result of
homology or analogy
• Homology is similarity due to shared ancestry
• Analogy is similarity due to convergent evolution
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• Convergent evolution occurs when similar
environmental pressures and natural selection
produce similar (analogous) adaptations in
organisms from different evolutionary lineages
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Analogous structures or molecular sequences that
evolved independently are also called
homoplasies
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Evaluating Molecular Homologies
• Systematists use computer programs and
mathematical tools when analyzing comparable
DNA segments from different organisms
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LE 25-6
1
2
Deletion
1
2
Insertion
1
2
1
2
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Concept 25.2: Phylogenetic systematics connects
classification with evolutionary history
• Taxonomy is the ordered division of organisms
into categories based on characteristics used to
assess similarities and differences
• In 1748, Carolus Linnaeus published a system of
taxonomy based on resemblances.
• Two key features of his system remain useful
today: two-part names for species and hierarchical
classification
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Binomial Nomenclature
• The 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 (not the
specific epithet alone)
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Hierarchical Classification
• Linnaeus introduced a system for grouping
species in increasingly broad categories
Animation: Classification Schemes
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LE 25-8
Panthera
pardus
Species
Panthera
Genus
Felidae
Family
Carnivora
Order
Mammalia
Class
Chordata
Phylum
Animalia
Kingdom
Domain
Eukarya
Linking Classification and Phylogeny
• Systematists depict evolutionary relationships in
branching phylogenetic trees
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Species
Mephitis
mephitis
(striped skunk)
Lutra lutra
(European
otter)
Genus
Panthera
Mephitis
Lutra
Felidae
Order
Panthera
pardus
(leopard)
Family
LE 25-9
Mustelidae
Carnivora
Canis
familiaris
(domestic dog)
Canis
lupus
(wolf)
Canis
Canidae
• Each branch point represents the divergence of
two species
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LE 25-UN497
Leopard
Domestic cat
Common ancestor
Wolf
Leopard
Domestic cat
Common ancestor
• “Deeper” branch points represent progressively
greater amounts of divergence
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Concept 25.3: Phylogenetic systematics informs the construction
of phylogenetic trees based on shared characteristics
• A cladogram depicts patterns of shared
characteristics among taxa
• A clade is a group of species that includes an
ancestral species and all its descendants
• Cladistics studies resemblances among clades
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Cladistics
• Clades can be nested in larger clades, but not all
groupings or organisms qualify as clades
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• A valid clade is monophyletic, signifying that it
consists of the ancestor species and all its
descendants
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LE 25-10a
Grouping 1
Monophyletic
• A paraphyletic grouping consists of an ancestral
species and some, but not all, of the descendants
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LE 25-10b
Grouping 2
Paraphyletic
• A polyphyletic grouping consists of various species
that lack a common ancestor
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LE 25-10c
Grouping 3
Polyphyletic
Shared Primitive and Shared Derived Characteristics
• In cladistic analysis, clades are defined by their
evolutionary novelties
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• A shared primitive character is a character that is
shared beyond the taxon we are trying to define
• A shared derived character is an evolutionary
novelty unique to a particular clade
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Outgroups
• 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 primitive characteristics
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• Outgroup comparison assumes that homologies
shared by the outgroup and ingroup must be
primitive characters that predate the divergence of
both groups from a common ancestor
• It enables us to focus on characters derived at
various branch points in the evolution of a clade
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-11
Leopard
Turtle
Salamander
Tuna
Lamprey
Lancelet
(outgroup)
TAXA
CHARACTERS
Hair
Amniotic (shelled) egg
Four walking legs
Hinged jaws
Vertebral column
(backbone)
Character table
Turtle
Leopard
Hair
Salamander
Amniotic egg
Tuna
Four walking legs
Lamprey
Hinged jaws
Lancelet (outgroup)
Vertebral column
Cladogram
Phylogenetic Trees and Timing
• Any chronology represented by the branching of a
phylogenetic tree is relative rather than absolute in
representing timing of divergences
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Phylograms
• In a phylogram, the length of a branch in a
cladogram reflects the number of genetic changes
that have taken place in a particular DNA or RNA
sequence in that lineage
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-12
Ultrametric Trees
• Branching in an ultrametric tree is the same as in
a phylogram, but all branches traceable from the
common ancestor to the present are equal length
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Millions of
years ago
Neoproterozoic
542
Paleozoic
251
Mesozoic
65.5
Cenozoic
LE 25-13
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The most parsimonious tree requires the fewest
evolutionary events to have occurred in the form
of shared derived characters
• 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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-14
Human
Mushroom
Tulip
0
30%
40%
0
40%
Human
Mushroom
Tulip
0
Percentage differences between sequences
25%
15%
15%
20%
15%
10%
5%
Tree 1: More likely
Comparison of possible trees
5%
Tree 2: Less likely
• In considering possible phylogenies for a group of
species, systematists compare molecular data for
the species.
• The most efficient way to study hypotheses is to
consider the most parsimonious hypothesis, the
one requiring the fewest evolutionary events
(molecular changes)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-15ab
Sites in DNA sequence
1 2 3 4 5 6 7
I
Species
II
III
IV
I
II
III
IV
Bases at
site 1 for
each species
Base-change
event
Phylogenetic Trees as Hypotheses
• The best hypotheses for phylogenetic trees fit the
most data: morphological, molecular, and fossil
• Sometimes the best hypothesis is not the most
parsimonious
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-16
Lizard
Bird
Mammal
Four-chambered
heart
Mammal-bird clade
Lizard
Bird
Mammal
Four-chambered
heart
Four-chambered
heart
Lizard-bird clade
Concept 25.4: Much of 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
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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
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• Orthologous genes are genes found in a single
copy in the genome
• They can diverge only after speciation occurs
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LE 25-17a
Ancestral gene
Speciation
Orthologous genes
• 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, often adding new functions
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LE 25-17b
Ancestral gene
Gene duplication
Paralogous genes
Genome Evolution
• Orthologous genes are widespread and extend
across many widely varied species
• The widespread consistency in total gene number
in organisms indicates genes in complex
organisms are very versatile and that each gene
can perform many functions
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Concept 25.5: Molecular clocks help track
evolutionary time
• To extend molecular phylogenies beyond the fossil
record, we must make an assumption about how
change occurs over time
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Molecular Clocks
• The molecular clock is a yardstick for measuring
absolute time of evolutionary change based on the
observation that some genes and other regions of
genomes seem to evolve at constant rates
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Applying a Molecular Clock: The Origin of HIV
• Phylogenetic analysis shows that HIV is
descended from viruses that infect chimpanzees
and other primates
• Comparison of HIV samples throughout the
epidemic shows that the virus evolved in a very
clocklike way
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The Universal Tree of Life
• The tree of life is divided into three great clades
called domains: Bacteria, Archaea, and Eukarya
• The early history of these domains is not yet clear
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings