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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
• 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
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
• Convergent evolution occurs when similar environmental
pressures and natural selection produce similar
(analogous) adaptations in organisms from different
evolutionary lineages
• Analogous structures or molecular sequences that evolved
independently are also called homoplasies
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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 latinized
• Both parts together name the species (not the
specific epithet alone)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-8
Panthera
pardus
Species
Panthera
Genus
Felidae
Family
Carnivora
Order
Mammalia
Class
Chordata
Phylum
Animalia
Kingdom
Domain
Eukarya
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
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Cladistics
• Clades can be nested in larger clades, but not all
groupings or organisms qualify as clades
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-10a
Grouping 1
•A valid clade is monophyletic, signifying that it
consists of the ancestor species and all its
descendants
Monophyletic
• A paraphyletic grouping consists of an ancestral
species and some, but not all, of the descendants
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-10b
Grouping 2
Paraphyletic
• A polyphyletic grouping consists of various species
that lack a common ancestor
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
LE 25-10c
Grouping 3
Polyphyletic
• 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
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
• 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
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
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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