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Chapter 25
Phylogeny & Systematics
Phylogeny
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the evolutionary history of a species or a group of
related species
the construction of phylogenies is based on:
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the fossil record (the sequence in which fossils appear
in the layers of sedimentary rock)
morphological & molecular homologies
Systematics
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an analytical approach to understanding the
diversity & relationships of organisms
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traditional systematics – uses morphological homologies
to infer evolutionary relationships
molecular systematics – uses molecular homologies
(similarities in DNA, RNA, proteins, & other molecules)
to infer evolutionary relationships
What are homologies?
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similarities between two
species due to shared ancestry
result of divergent evolution
can be:
 shared derived characters – features that
are unique to a particular taxon (classification
group)
 shared primitive characters – features that
a group of organisms may share with other
organisms outside their taxon (ie: with
organisms that they are not as closely related
to)
Analogies
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similarities between two unrelated species that
evolved independently of each other as 2
lineages adapted to similar lifestyles
result of convergent evolution
 (ex) 4-chambered heart
of birds & mammals
NOTE: the more points of resemblance 2
characteristics (ex: skulls, DNA sequences) have
the less likely they are analogies ( the more
likely they are homologies)
Taxonomy

the science of classification
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ordered division of organisms into categories
based on a set of characteristics used to assess
similarities (shared derived characters) &
differences
features of taxonomy useful in phylogenetic
systematics:
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binomial nomenclature
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Genus species names used to describe species
hierarchical classification
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includes 8 taxa: DKPOCFGS
Phylogenetic Trees
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diagrams that depict
hypotheses about
evolutionary
relationships
the branches of
phylogenetic trees
reflect the hierarchical
classifications of
groups nested within
more inclusive groups
the sequence of the
branching is NOT
related to the age of
the species
Cladograms
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
diagrams that depict patterns
of shared characteristics
among taxa
do not imply evolutionary
history but if the shared
characteristics are due to
common ancestry, can form
the basis of a phylogenetic
tree
Clades
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groupings within a cladogram
clades can be:
 monophyletic – made up of an ancestral
species and all of its descendents
 paraphyletic – made up of an ancestral
species and only some of its descendents
 polyphyletic – a grouping that leaves out the
common ancestor of the species included
Cladistics

the analysis of how species may be
grouped into clades
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monophyletic clades (valid clades) are defined
by characteristics that are unique to the group
(shared derived characteristics)
these characteristics are identified by
comparing ingroup species with an outgroup
species that does not have the shared derived
characteristic
Phylogenetic Trees & Rate of Evolution
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by varying the lengths of the
branches in a phylogenetic
tree, we can show the rate at
which a homologous gene (a
shared gene due to common
ancestry) has evolved in
different lineages
this type of diagram is called
a phylogram
Phylogenetic Trees & Geologic Time
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another way phylogenetic trees
can be altered is to place
evolutionary branch points in the
context of geologic time
this type of diagram is called an
ultrametric tree
the ultrametric tree to the right
shows us that invertebrates &
chordates diverged during the
Neoproterozoic Era and the two
groups have had an equal
amount of type to evolve since
then (even if the rates of
evolution within the lineages are
different)
Which phylogenetic tree is most accurate?
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as we increase the number of species included in
a phylogenetic tree, the number of ways to
arrange them also increases leading to many
different phylogenetic hypotheses
the 1st step in evaluating phylogenetic
hypotheses is to follow the principle of maximum
parsimony:
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the simplest explanation that is consistent with the
facts should be investigated first
in other words, investigate the phylogenetic tree
that requires the fewest evolutionary changes first
the 2nd step is to apply the principle of maximum
likelihood

investigate the phylogenetic tree that reflects the
most likely sequence of evolutionary events (based
on certain rules about how DNA changes over time)
Types of Homologous Genes
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orthologous genes
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genes that are passed in a straight line from one
generation to the next but have ended up in different
gene pools because of speciation
often shared by distantly related species
(ex) 99% of the genes of humans & mice and 50% of the
genes of humans & yeast are orthologous
paralogous genes
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genes found in multiple copies within the same genome
results from gene duplication
may lead to gene families that have related functions
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(ex) the -globin & -globin gene families (which both
produce subunits of hemoglobin) diverged from an ancestral
globin gene that likely duplicated and, then, mutated
often shared by closely related organisms
studying both types can give us clues to an
organism’s evolutionary history
Molecular Clock
method used to measure the absolute
time (ie: the numerical age in mya) of
evolutionary change based on the
observation that some genes & other
regions of the genome appear to evolve at
constant rates
 based on the assumption that the number
of nucleotides substituted in genes is
proportional to the amount of time since…
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a species branched from its common ancestor
(orthologous)
the genes duplicated (paralogous)
Preview: Universal Tree of Life
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consists of 3 domains:
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Bacteria
Archaea
Eukarya
early history unclear