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
• This chapter describes how biologists trace
phylogeny
– The evolutionary history of a species or group
of related species
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Biologists draw on the fossil record
– Which provides information about ancient
organisms
Figure 25.1
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Biologists also use systematics
– As an analytical approach to understanding the
diversity and relationships of organisms, both
present-day and extinct
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Currently, systematists use
– Morphological, biochemical, and molecular
comparisons to infer evolutionary relationships
Figure 25.2
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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Fossil Record
• Sedimentary rocks
– Are the richest source of fossils
– Are deposited into layers called strata
1 Rivers carry sediment to the
ocean. Sedimentary rock layers
containing fossils form on the
ocean floor.
2 Over time, new strata are
deposited, containing fossils
from each time period.
3 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
Figure 25.3
Older stratum
with older fossils
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Though sedimentary fossils are the most
common
– Paleontologists study a wide variety of fossils
(c) Leaf fossil, about 40 million years old
(b) Petrified tree in Arizona, about
190 million years old
(a) Dinosaur bones being excavated
from sandstone
(d) Casts of ammonites,
about 375 million
years old
(f) Insects
preserved
whole in
amber
Figure 25.4a–g
(g) Tusks of a 23,000-year-old mammoth,
frozen whole in Siberian ice
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
(e) Boy standing in a 150-million-year-old
dinosaur track in Colorado
Morphological and Molecular Homologies
• In addition to fossil organisms
– Phylogenetic history can be inferred from
certain morphological and molecular
similarities among living organisms
• In general, organisms that share 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
• A potential misconception in constructing a
phylogeny
– Is similarity due to convergent evolution, called
analogy, rather than shared ancestry
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Convergent evolution occurs when similar
environmental pressures and natural selection
– Produce similar (analogous) adaptations in
organisms from different evolutionary lineages
Figure 25.5
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Analogous structures or molecular sequences
that evolved independently
– Are also called homoplasies
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Evaluating Molecular Homologies
• Systematists use computer programs and
mathematical tools
– When analyzing comparable DNA segments from
different organisms
1
Ancestral homologous
DNA segments are
identical as species 1
and species 2 begin to
diverge from their
common ancestor.
1 C C A T C A G A G T C C
2 C C A T C A G A G T C C
A C G G A T A G T C C A C T A G G C A C T A
T C A C C G A C A G G T C T T T G A C T A G
Deletion
2
3
4
Figure 25.6
Deletion and insertion
mutations shift what
had been matching
sequences in the two
species.
Homologous regions
(yellow) do not all align
because of these mutations.
Homologous regions
realign after a computer
program adds gaps in
sequence 1.
1
C C A T C A G A G T C C
2
C C A T C A G A G T C C
G T A
Insertion
1
C C A T
C A
2
C C A T
G T A
1
2
A G T C C
C C A T
C C A T
G T A
C A G
A G T C C
C A
A G T C C
C A G
A G T C C
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Figure 25.7
• Concept 25.2: Phylogenetic systematics
connects classification with evolutionary history
• Taxonomy
– Is the ordered division of organisms into
categories based on a set of characteristics
used to assess similarities and differences
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Binomial Nomenclature
• Binomial nomenclature
– Is the two-part format of the scientific name of
an organism
– Was developed by Carolus Linnaeus
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The binomial name of an organism or scientific
epithet
– Is latinized
– Is the genus and species
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Hierarchical Classification
• Linnaeus also introduced a system
– For grouping species in increasingly broad
categories
Panthera
Species pardus
Panthera
Genus
Felidae
Family
Carnivora
Order
Class
Phylum
Kingdom
Figure 25.8
Domain
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Mammalia
Chordata
Animalia
Eukarya
Linking Classification and Phylogeny
• Systematists depict evolutionary relationships
Species
Panthera
Order
Family
Panthera
Mephitis
Canis
Canis
Lutra lutra
pardus
mephitis
familiaris
lupus
(European
(leopard) (striped skunk)
(domestic dog) (wolf)
otter)
Genus
– In branching phylogenetic trees
Mephitis
Felidae
Lutra
Mustelidae
Carnivora
Figure 25.9
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Canis
Canidae
• Each branch point
– Represents the divergence of two species
Leopard
Domestic cat
Common ancestor
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• “Deeper” branch points
– Represent progressively greater amounts of
divergence
Wolf
Leopard
Common ancestor
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Domestic cat
• Concept 25.3: Phylogenetic systematics informs the
construction of phylogenetic trees based on shared
characteristics
• A cladogram
– Is a depiction of patterns of shared characteristics
among taxa
• A clade within a cladogram
– Is defined as a group of species that includes an
ancestral species and all its descendants
• Cladistics
– Is the study of resemblances among clades
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Cladistics
• Clades
– Can be nested within larger clades, but not all
groupings or organisms qualify as clades
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• A valid clade is monophyletic
– Signifying that it consists of the ancestor
species and all its descendants
Grouping 1
E
D
J
H
G
F
C
K
I
B
A
Figure 25.10a
(a) Monophyletic. In this tree, grouping 1,
consisting of the seven species B–H, is a
monophyletic group, or clade. A monophyletic group is made up of an
ancestral species (species B in this case)
and all of its descendant species. Only
monophyletic groups qualify as
legitimate taxa derived from cladistics.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• A paraphyletic clade
– Is a grouping that consists of an ancestral
species and some, but not all, of the
descendants
Grouping 2
G
E
D
C
J
H
K
I
F
B
A
Figure 25.10b
(b) Paraphyletic. Grouping 2 does not
meet the cladistic criterion: It is
paraphyletic, which means that it
consists of an ancestor (A in this case)
and some, but not all, of that ancestor’s
descendants. (Grouping 2 includes the
descendants I, J, and K, but excludes
B–H, which also descended from A.)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• A polyphyletic grouping
– Includes numerous types of organisms that
lack a common ancestor
Grouping 3
D
E
G
J
H
I
F
C
K
B
A
Figure 25.10c
(c) Polyphyletic. Grouping 3 also fails the
cladistic test. It is polyphyletic, which
means that it lacks the common ancestor
of (A) the species in the group. Furthermore, a valid taxon that includes the
extant species G, H, J, and K would
necessarily also contain D and E, which
are also descended from A.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Shared Primitive and Shared Derived Characteristics
• In cladistic analysis
– Clades are defined by their evolutionary
novelties
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• A shared primitive character
– Is a homologous structure that predates the
branching of a particular clade from other
members of that clade
– Is shared beyond the taxon we are trying to
define
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• A shared derived character
– Is an evolutionary novelty unique to a
particular clade
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Outgroups
• Systematists use a method called outgroup
comparison
– To differentiate between shared derived and
shared primitive characteristics
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• As a basis of comparison we need to designate
an outgroup
– which is a species or group of species that is
closely related to the ingroup, the various
species we are studying
• Outgroup comparison
– Is based on the assumption that homologies
present in both the outgroup and ingroup must
be primitive characters that predate the
divergence of both groups from a common
ancestor
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• The outgroup comparison
– Enables us to focus on just those characters
that were derived at the various branch points
in the evolution of a clade
Lamprey
Tuna
Salamander
Turtle
Leopard
Hair
0
0
0
0
0
1
Amniotic (shelled) egg
0
0
0
0
1
1
Four walking legs
0
0
0
1
1
1
Hinged jaws
0
0
1
1
1
1
Vertebral column (backbone)
0
1
1
1
1
1
CHARACTERS
Lancelet
(outgroup)
TAXA
Turtle
Salamander
(a) Character table. A 0 indicates that a character is absent; a 1
indicates that a character is present.
Leopard
Hair
Amniotic egg
Tuna
Lamprey
Four walking legs
Hinged jaws
Lancelet (outgroup)
Figure 25.11a, b
Vertebral column
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
(b) Cladogram. Analyzing the distribution of these
derived characters can provide insight into vertebrate
phylogeny.
Phylogenetic Trees and Timing
• Any chronology represented by the branching
pattern of a phylogenetic tree
– Is relative rather than absolute in terms of
representing the 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
Figure 25.12
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Ultrametric Trees
In an ultrametric tree
The branching pattern is the same as in a phylogram, but all the
branches that can be traced from the common ancestor to the
present are of equal length
Millions of
years ago
Proterozoic
542
Paleozoic
251
Mesozoic
Cenozoic
–
65.5
•
Figure 25.13
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Maximum Parsimony and Maximum Likelihood
• Systematists
– Can never be sure of finding the single best
tree in a large data set
– Narrow the possibilities by applying the
principles of maximum parsimony and
maximum likelihood
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Among phylogenetic hypotheses
– The most parsimonious tree is the one that
requires the fewest evolutionary events to
have occurred in the form of shared derived
characters
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Applying parsimony to a problem in molecular
systematics
Human
Human
0
Mushroom
Mushroom
Tulip
30%
0
Tulip
Figure 25.14
(a) Percentage differences between sequences
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
40%
40%
0
• Applying parsimony to a problem in molecular
systematics
25%
15%
15%
15%
20%
10%
5%
5%
Tree 1: More likely
Figure 25.14
(b) Comparison of possible trees
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Tree 2: Less 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
APPLICATION In considering possible phylogenies for a group of species, systematists compare molecular data for the species. The most efficient way to study the various phylogenetic
hypotheses is to begin by first considering the most parsimonious—that is, which hypothesis requires the fewest total evolutionary events (molecular changes) to have occurred.
TECHNIQUE
1
Follow the numbered steps as we apply the principle of parsimony to a hypothetical phylogenetic problem involving four closely related bird species.
First, draw the possible phylogenies for the species
(only 3 of the 15 possible trees relating these four
species are shown here).
Species
I
I
II
III
I
IV
Species
IV
Species
III
Species
II
II
III
I
IV
II
IV
Three possible phylogenetic hypothese
1
2
Tabulate the molecular data for the species (in this simplified
example, the data represent a DNA sequence consisting of
just seven nucleotide bases).
I
A
G
G
G
G
G
T
II
G
G
G
A
G
G
G
III
G
A
G
G
A
A
T
IV
G
G
A
G
A
A
G
I
A
II
G
Species
3
Figure 25.15a
Now focus on site 1 in the DNA sequence. A single basechange event, marked by the crossbar in the branch leading
to species I, is sufficient to account for the site 1 data.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Sites in DNA sequence
2
5 6
3 4
7
III
G
G
Base-change
event
IV
G
G
G
Bases at
site 1 for
each species
III
4 Continuing the comparison of bases at sites 2, 3, and 4
reveals that each of these possible trees requires a total of
four base-change events (marked again by crossbars).
Thus, the first four sites in this DNA sequence do not help
us identify the most parsimonious tree.
5 After analyzing sites 5 and 6, we find that the first tree requires
fewer evolutionary events than the other two trees (two base
changes versus four). Note that in these diagrams, we assume
that the common ancestor had GG at sites 5 and 6. But even if
we started with an AA ancestor, the first tree still would require
only two changes, while four changes would be required to make
the other hypotheses work. Keep in mind that parsimony only
considers the total number of events, not the particular nature of
the events (how likely the particular base changes are to occur).
I
II
I
II
GG GG
III
IV
III
AA
IV
AA
I
III
GG AA
AA
GG
GG
I
T
II
G
III
Two base
changes
GG
6 At site 7, the three trees also differ in the number of
evolutionary events required to explain the DNA data.
I
III
T
IV
G
T
T
Figure 25.15b
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I
II
IV
II
GG
IV
AA
I
IV
GG AA
GG
GG
I
IV
I
T
III
T
8 events
IV
II
G
IV
G
G
T
I
III
III
II
GG
III
AA
GG
I
T
IV
G
II
G
III
T
T
T
T
III
II
GG
GG
T
RESULTS
To identify the most parsimonious tree, we total
all the base-change events noted in steps 3–6 (don’t forget to
include the changes for site 1, on the facing page). We conclude
that the first tree is the most parsimonious of these three possible
phylogenies. (But now we must complete our search by
investigating the 12 other possible trees.)
II
T
II
9 events
IV
I
IV
II
10 events
III
Phylogenetic Trees as Hypotheses
• The best hypotheses for phylogenetic trees
– Are those that fit the most data: morphological,
molecular, and fossil
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Sometimes there is compelling evidence
– That the best hypothesis is not the most
parsimonious
Bird
Lizard
Mammal
Four-chambered
heart
(a) Mammal-bird clade
Bird
Lizard
Mammal
Four-chambered
heart
Four-chambered
heart
Figure 25.16a, b
(b) Lizard-bird clade
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• 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
Gene Duplications and Gene Families
• Gene duplication
– Is one of the most important types of mutation
in evolution because it increases the number
of genes in the genome, providing further
opportunities for evolutionary changes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Orthologous genes
– Are genes found in a single copy in the
genome
– Can diverge only once speciation has taken
place
Ancestral gene
Speciation
(a)
Orthologous genes
Figure 25.17a
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Paralogous genes
– Result from gene duplication, so they are
found in more than one copy in the genome
– Can diverge within the clade that carries them,
often adding new functions
Ancestral gene
Gene duplication
Figure 25.17b
(b)
Paralogous genes
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Genome Evolution
• Orthologous genes are widespread
– And extend across many widely varied species
• The widespread consistency in total gene
number in organisms of varying complexity
– Indicates that genes in complex organisms are
extremely versatile and that each gene can
perform many functions
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Concept 25.5: Molecular clocks help track
evolutionary time
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Molecular Clocks
• The molecular clock
– Is a yardstick for measuring the absolute time
of evolutionary change based on the
observation that some genes and other
regions of genomes appear 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
– And 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
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
• A comparison of HIV samples from throughout
the epidemic
– Has shown that the virus has evolved in a
remarkably clocklike fashion
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
Billion years ago
Bacteria
Eukarya Archaea
0
4
Symbiosis of
chloroplast
ancestor with
ancestor of green
plants
1
3
Symbiosis of
mitochondrial
ancestor with
ancestor of
eukaryotes
2
Possible fusion
of bacterium
and archaean,
yielding
ancestor of
eukaryotic cells
1
Last common
ancestor of all
living things
4
2
3
2
3
1
Origin of life
Figure 25.18
4
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings