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25
Reconstructing and Using
Phylogenies
25 Reconstructing and Using Phylogenies
• 25.1 What Is Phylogeny?
• 25.2 How Are Phylogenetic Trees
Constructed?
• 25.3 How Do Biologists Use Phylogenetic
Trees?
• 25.4 How Does Phylogeny Relate to
Classification?
25.1 What Is Phylogeny?
Phylogeny is a description of the
evolutionary history of relationships
among organisms.
This is portrayed in a diagram called a
phylogenetic tree.
Each split or node represents the point at
which lineages diverged. The common
ancestor of all organisms in the tree is
the root.
Figure 25.1 How to Read a Phylogenetic Tree (Part 1)
Figure 25.1 How to Read a Phylogenetic Tree (Part 2)
25.1 What Is Phylogeny?
The timing of divergences is shown by
the position of nodes on a time or
divergence axis.
Lineages can be rotated around nodes;
the vertical order of taxa is largely
arbitrary.
25.1 What Is Phylogeny?
A taxon (plural taxa) is any group of
species that we designate (e.g.,
vertebrates).
A taxon that consists of all the
descendents of a common ancestor is
called a clade.
25.1 What Is Phylogeny?
Two species that are each other’s closest
relatives are sister species.
Two clades that are each other’s closest
relatives are sister clades.
Phylogenetic trees were used mainly in
systematics (study of biodiversity); but
are now used in nearly all fields of
biology.
25.1 What Is Phylogeny?
One of the greatest unifying concepts in
biology is that all life is connected
through evolutionary history.
The “Tree of Life” is the complete, 4billion-year history of life.
Knowledge of evolutionary relationships
is essential for making comparisons in
biology.
25.1 What Is Phylogeny?
Biologists determine traits that differ
within a group of interest, then try to
determine when these traits evolved.
Often, we wish to know how the trait was
influenced by environmental conditions
or selection pressures.
25.1 What Is Phylogeny?
Features shared by two or more species
that were inherited from a common
ancestor are homologous.
Example: The vertebral column is
homologous in all vertebrates.
25.1 What Is Phylogeny?
A trait that differs from the ancestral trait
is called derived.
A trait that was present in the ancestor of
a group is ancestral.
25.1 What Is Phylogeny?
Derived traits that are shared among a
group and are viewed as evidence of
the common ancestry of the group are
known as synapomorphies.
The vertebral column is a synapomorphy
of all vertebrates.
25.1 What Is Phylogeny?
Similar traits can develop in unrelated
groups of organisms:
• Convergent evolution—independently
evolved traits subjected to similar
selection pressures may become
superficially similar.
Example: the wings of bats and birds
Figure 25.2 The Bones Are Homologous; the Wings Are Not
25.1 What Is Phylogeny?
• Evolutionary reversal—a character
reverts from a derived state back to the
ancestral state.
Example: Most frogs do not have lower
teeth, but the ancestor of frogs did.
One frog genus has regained teeth in
the lower jaw.
25.1 What Is Phylogeny?
Traits that are similar for reasons other
than inheritance from a common
ancestor are called homoplastic traits or
homoplasies.
Traits may be ancestral or derived,
depending on the point of reference in
phylogeny. Bird feathers are ancestral in
birds, but derived when considering all
living vertebrates.
25.2 How Are Phylogenetic Trees Constructed?
Constructing a phylogenetic tree using
eight vertebrate animals:
Assume no convergent evolution; and no
derived traits have been lost.
Lampreys are the outgroup—any species
or group outside the group of interest.
The group of interest is the ingroup.
Comparison with the outgroup shows
which traits of the ingroup are derived
and which are ancestral.
Table 25.1 (Part 1)
Table 25.1 (Part 2)
25.2 How Are Phylogenetic Trees Constructed?
Chimpanzees and mice share two
derived traits—fur and mammary
glands. Assume these traits evolved
only once; they are synapomorphies for
this group.
Keratinous scales are a synapomorphy of
the crocodile, pigeon, and lizard.
Information about the synapomorphies
allows construction of the tree.
Figure 25.3 Inferring a Phylogenetic Tree
25.2 How Are Phylogenetic Trees Constructed?
Phylogenetic trees are typically
constructed using hundreds or
thousands of traits.
How are synapomorphies and
homoplasies determined?
25.2 How Are Phylogenetic Trees Constructed?
The parsimony principle: the simplest
explanation of observed data is the
preferred explanation.
Minimize the number of evolutionary
changes that must be assumed—the
fewest homoplasies.
Occam’s razor: the best explanation fits
the data with the fewest assumptions.
25.2 How Are Phylogenetic Trees Constructed?
Computer programs are now used to
analyze traits and construct trees.
All kinds of traits—morphological, fossil,
developmental, molecular, behavioral—
are used by systematists to construct
phylogenies.
25.2 How Are Phylogenetic Trees Constructed?
Morphology
Most species have been described on
the basis of morphological data, such as
features of the skeletal system in
vertebrates, or floral structures in plants.
Limitations: comparing distantly related
species; some morphological variation
is caused by environment; some
species show few morphological
differences.
25.2 How Are Phylogenetic Trees Constructed?
Development
Similarities in development patterns may
reveal evolutionary relationships.
Example: Sea squirts and vertebrates all
have a notochord at some time in their
development.
Figure 25.4 A Larva Reveals Evolutionary Relationships
25.2 How Are Phylogenetic Trees Constructed?
Paleontology
Fossils provide information about the
morphology of past organisms, and
where and when they lived.
Important in determining derived and
ancestral traits, and when lineages
diverged.
Limitations: fossil record is fragmentary
and missing for some groups.
25.2 How Are Phylogenetic Trees Constructed?
Behavior
Behavior can be inherited or culturally
transmitted.
Bird songs are often learned, and may
not be a useful trait for phylogenies.
Frog calls are genetically determined and
can be used in phylogenetic trees.
25.2 How Are Phylogenetic Trees Constructed?
Molecular data
DNA sequences have become the most
widely used data for constructing
phylogenetic trees.
Mitochondrial and chloroplast DNA is
used as well as nuclear DNA.
Gene product information, such as amino
acid sequences, are also used.
25.2 How Are Phylogenetic Trees Constructed?
Mathematical models are used to
describe DNA changes over time.
Models can be used to compute
maximum likelihood solutions, the
probability of the observed data
evolving on the specified tree.
Most often used for molecular data,
models of evolutionary change are
easier to develop.
25.2 How Are Phylogenetic Trees Constructed?
Testing the accuracy of phylogenetic
reconstructions: experiments with living
organisms and computer simulations.
Cultures of bacteriophage T7 were grown
in the presence of a mutagen and
allowed to evolve in the laboratory.
Figure 25.5 A Demonstration of the Accuracy of Phylogenetic Analysis (Part 1)
Figure 25.5 A Demonstration of the Accuracy of Phylogenetic Analysis (Part 2)
25.2 How Are Phylogenetic Trees Constructed?
At the end of the experiment, genomes of
the endpoints were sequenced and
investigators built phylogenetic trees
that accurately reflected the known
evolutionary history of the cultures.
25.2 How Are Phylogenetic Trees Constructed?
Phylogenetic methods can be used to
reconstruct traits or nucleotide
sequences for ancestral species.
Example: Reconstruction of opsin
(pigment involved in vision) in the
ancestral archosaur (last common
ancestor of birds, crocodiles, and
dinosaurs).
25.2 How Are Phylogenetic Trees Constructed?
Analysis of opsin from living vertebrates
was used to estimate the amino acid
sequence of opsin in the archosaur.
A protein of this sequence was
constructed in the laboratory and then
wavelengths of light it absorbs were
measured.
Activity in the red range indicated that the
animal may have been nocturnal.
25.2 How Are Phylogenetic Trees Constructed?
Molecular clock hypothesis: Rates of
molecular change are constant enough
to predict timing of evolutionary
divergence.
Among closely related species, a given
gene usually evolves at a reasonably
constant rate, and can be used to
determine time elapsed since a
divergence.
25.2 How Are Phylogenetic Trees Constructed?
Molecular clocks must be calibrated
using independent data, such as the
fossil record, and known divergences or
biogeographic dates (e.g., from
continental drift).
Example: 500 species of cichlid fishes of
Lake Victoria.
25.2 How Are Phylogenetic Trees Constructed?
Mitochondrial DNA sequences were used to
construct a phylogenetic tree of the
cichlids.
It has been suggested that the ancestors
came from the older Lake Kivu, and they
colonized Lake Victoria on two occasions.
Molecular clock analysis suggested that
some endemic cichlid lineages split at
least 100,000 years ago.
25.2 How Are Phylogenetic Trees Constructed?
The analyses suggest that Lake Victoria
did not dry up completely between
15,600 and 14,700 years ago, and
many species survived in rivers and in
the remnants of the lake during the dry
period.
Figure 25.6 Origins of the Cichlid Fishes of Lake Victoria (Part 1)
Figure 25.6 Origins of the Cichlid Fishes of Lake Victoria (Part 2)
25.3 How Do Biologists Use Phylogenetic Trees?
Most flowering plants reproduce by
outcrossing or mating with another
individual.
Other plants are selfing, which requires
that they be self-compatible.
Phylogenetic analysis can show how
often self-compatibility has evolved.
25.3 How Do Biologists Use Phylogenetic Trees?
The genus Linanthus has a variety of
breeding systems.
Outcrossing species have long petals
and are self-incompatible. Selfcompatible species have short petals.
A phylogeny was constructed using
ribosomal DNA.
Self-incompatibility is the ancestral state.
Figure 25.7 Phylogeny of a Section of the Plant Genus Linanthus (Part 1)
Figure 25.7 Phylogeny of a Section of the Plant Genus Linanthus (Part 2)
25.3 How Do Biologists Use Phylogenetic Trees?
Phylogenetic analysis can be important in
understanding zoonotic diseases
(infectious organisms are transmitted to
humans from another animal host).
Example: HIV was acquired from
chimpanzees and sooty mangabeys.
Figure 25.8 Phylogenetic Tree of Immunodeficiency Viruses
25.3 How Do Biologists Use Phylogenetic Trees?
Reproductive success of male swordtails
is associated with long “swords” (sexual
selection). Evolution of the sword may
result from a preexisting bias of female
sensory systems—sensory exploitation
hypothesis.
Phylogenetics identified platyfishes as
the closest relatives.
25.3 How Do Biologists Use Phylogenetic Trees?
Artificial swords were attached to
platyfish males.
Female platyfish preferred males with the
artificial swords, supporting the idea that
females had a preexisting bias even
before the swords evolved.
Figure 25.9 The Origin of a Sexually Selected Trait in the Fish Genus Xiphophorus
25.3 How Do Biologists Use Phylogenetic Trees?
Rate of evolution of influenza virus is
high.
Phylogenetic analysis indicates there is a
strong selection by the human immune
system for most strains.
Only strains with the greatest number of
substitutions on hemagglutinin (surface
protein recognized by the immune
system) are likely to leave descendents.
Figure 25.10 Model of Hemagglutinin, a Surface Protein of Influenza
25.3 How Do Biologists Use Phylogenetic Trees?
Phylogenetic analysis helps biologists
predict which of the currently circulating
strains are most likely to survive and
leave descendents.
This information is then used to formulate
influenza vaccines.
25.4 How Does Phylogeny Relate to Classification?
The biological classification system was
started by Swedish biologist Carolus
Linnaeus in the 1700s.
Binomial nomenclature gives every
species a unique, unambiguous name.
Figure 25.11 Many Different Plants Are Called Bluebells
25.4 How Does Phylogeny Relate to Classification?
Every species has two names: the genus
(group of closely related species) to
which it belongs, and the species
name.
The name of the taxonomist who first
described the species is often included.
Example: Homo sapiens Linnaeus
25.4 How Does Phylogeny Relate to Classification?
A taxon is any group of organisms that is
treated as a unit, such as a genus, or all
insects.
Species and genera are further grouped
into a hierarchical classification system.
Genera are grouped into families (e.g.,
the family Rosaceae includes the genus
Rosa and its close relatives).
25.4 How Does Phylogeny Relate to Classification?
Families are grouped into orders
Orders into classes
Classes into phyla
Phyla into kingdoms
Application of these levels is somewhat
subjective.
25.4 How Does Phylogeny Relate to Classification?
Biological classifications are used to
express the evolutionary relationships of
organisms.
Taxa are expected to be monophyletic:
a taxon contains an ancestor and all
descendents of that ancestor, and no
other organisms. Also known as a
clade.
25.4 How Does Phylogeny Relate to Classification?
But detailed phylogenetic information is
not always available.
A group that does not include its common
ancestor is polyphyletic.
A group that does not include all
descendents of a common ancestor is
paraphyletic.
25.4 How Does Phylogeny Relate to Classification?
A true clade or monophyletic group can
be removed from the tree by making a
single “cut.”
Taxonomists agree that polyphyletic and
paraphyletic groups are not appropriate
taxonomic units. These groups are
gradually being eliminated and
taxonomic classifications revised.
Figure 25.12 Monophyletic, Polyphyletic, and Paraphyletic Groups
25.4 How Does Phylogeny Relate to Classification?
Explicit rules govern the use of scientific
names.
Ensures that there is only one correct
scientific name for any taxon.
Different taxonomic rules have been
developed for zoology, botany, and
microbiology, but taxonomists are now
working towards common sets of rules.