Download Chapter 26 Presentation-Phylogeny and the Tree of Life

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A major step forward in the study of
bacteria was the recognition in 1977 by
Carl Woese that Archea have a separate
line of evolutionary descent from bacteria.
Famous scientists, including Luria and
Mayr, objected to his division of the
prokaryotes. To what extent is
conservatism in science desirable?
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Chapter 26
Cladistics
“Nothing is worse than active ignorance.”
--Goethe
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Essential Idea
The ancestry of groups of species can
be deduced by comparing their base or
amino acid sequences.
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Phylogeny and Systematics
Phylogeny is the piecing
together of the evolutionary
history of a species or a group
of species.
Phylogenies show evolutionary
relationships.
Sometimes we get unexpected
findings resulting in a
reclassification of a species or a
group of species.
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Phylogeny and Systematics
Systematics focuses on classifying
various organisms and seeks to
determine their evolutionary
relationships.
Systematists use data from a variety of
sources: fossils, molecules and genes are
main sources.
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Molecular Data
Evidence for which species are part of
a clade can be obtained from the base
of sequences of a gene or the
corresponding amino acid sequence of
a protein.
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Molecular Similarities
Molecular similarities
are DNA sequences
that indicate a degree
of relatedness
between organisms.
The more similar the
DNA sequences, the
more closely related
the organisms.
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Molecular Similarities
Sequence differences accumulate
gradually so there is a positive
correlation between the number of
differences between two species and
the time since they diverged from a
common ancestor.
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Molecular Similarities
Molecular similarities are often used to
explain events that occurred in the
evolution of organisms.
Icefish example.
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Homologies vs. Analogies
Traits can be said to be analogous or
homologous.
Homologies are similarities due to a
shared ancestry.
Morphological homologies, as we just
saw, are shared anatomical features
which perform a similar function.
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Homologies vs. Analogies
An analogy is a feature of two
organisms that is a result of convergent
evolution rather than decent from a
common ancestor.
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Homologies vs. Analogies
Take the burrowing moles of North
America and Australia as an example.
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Homoplasies
When evaluating relatedness, it is
important to look at homoplasies—the
coincidental matches that otherwise
different DNA sequences happen to
share.
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Homoplasies
Why might you expect organisms that
are not closely related to nevertheless
share roughly 25% of their bases?
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Phylogenetic Trees
These trees are branching diagrams that
show how organisms are related to one
another.
The shared characters of a phylogeny are
grouped into a branch of dichotomous
branching taxa.
The branches represent a divergence from
a common ancestor.
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Cladograms
A cladogram is a tree diagram that
shows the most probable sequence of
divergence in clades.
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Cladistics
Cladistics is the approach which uses the
common ancestry of an organism as the
primary criterion for classification.
Using this methodology, biologists place
organisms into groups called clades.
Cladists seek to classify all members of a
particular group of organisms into a particular
branch on a tree.
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A Clade
A clade is a group of organisms that
have evolved from a common ancestor.
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Monophyletic Clade
A monophyletic
clade consists of
an ancestral
species and all of
its descendants.
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A Paraphyletic Clade
This is a grouping
which lacks some
members.
It consists of an
ancestral species
and some, but not
all, of the
descendants.
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A Paraphyletic Clade
The members of a
paraphyletic clade
include those that have
changed little from the
ancestral state; those that
have changed more are
excluded.
A paraphyletic group
contains only the
conservative
descendants from an
ancestral species.
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A Polyphyletic Clade
Polyphyletic groups
are formed when
two lineages
convergently evolve
similar character
states.
Think of the
Australian and
North American
burrowing moles.
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A Polyphyletic Clade
Organisms
classified into the
same polyphyletic
group share
phenetic
homoplasies as
opposed to
homologies.
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A Polyphyletic Clade
In other words, C
is grouped with
DEFG because it
looks similar
(morphology) and
is assumed to be
somehow related.
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Cladistics
One of the unique things about
cladistics is that it has supplied
(molecular) evidence showing that the
classifications of some groups based
solely on structure did not correspond
with the evolutionary origins of a group
or species.
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Inferring Phylogenies
To build a phylogeny, we have to look at
various features of the organisms in
question.
We also have to take into account
shared ancestral characters and shared
derived characters.
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Inferring Phylogenies
A shared derived character is an evolutionary
novelty that is unique to a particular clade.
Example: Hair is a character shared by mammals,
but not found in non-mammalian vertebrates.
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Inferring Phylogenies
A shared ancestral character is any
character that is shared beyond the
taxon we are trying to define.
Example: the backbone is the homologous
structure that predates the branching of the
mammalian clade from other vertebrate clades.
NOTE: The backbone can qualify as a shared
derived character at a deeper branch point that
distinguishes all vertebrates from other animals.
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Inferring Phylogenies
Inferring phylogenies becomes difficult
when you have to sort through homologies
to determine shared ancestral and shared
derived characters.
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The Distinction Between Homologous
and Analogous Similarities
Among vertebrates, the backbone is a
shared primitive character because it
was present in a common ancestor to
all vertebrates.
However, among eukaryotes it is a
shared derived character because it is
an evolutionary novelty that is unique to
a particular clade.
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Ingroups vs. Outgroups
To draw comparisons and to
differentiate between shared derived
characters and shared primitive
characters, scientists use ingroups and
outgroups.
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Ingroups vs. Outgroups
The ingroup is the species we are
studying.
Outgroups comprise a species or group
of species that are closely related to the
group being studied, but not as closely
related as any of the study-group
members are to each other.
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Outgroups
For example, to
build the clade at
the right, we’re
going to examine 5
vertebrates: a
leopard, a turtle, a
salamander, a tuna,
and a lamprey.
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Outgroups
We use an outgroup
to serve as a basis
of comparison
which is a species
or group of species
closely related to
the ingroup—the
various species we
are studying.
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Outgroup
Recall, outgroup is less closely related than
any of the ingroup members are to each
other (based on the evidence).
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Outgroup
The lancet in our
example is the good
choice of an outgroup.
It is a member of the
phylum Chordata, but it
doesn’t have a
backbone.
We now build our
cladogram by comparing
the ingroup with the
outgroup.
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Outgroup Comparison
The outgroup
comparison is based
on the assumption
that homologies are
primitive characters
that predate the
divergence of both
groups—a notochord
in our example.
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Outgroup Comparison
Lancets have
notochords their
entire life,
vertebrates only
have them during
embryonic
development.
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Outgroup Comparison
The ingroup species
displays a mix of shared
primitive and shared
derived characters.
Using the outgroup
comparison, we can
compare only those
characters that were
derived at the various
branch points.
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Outgroup Comparison
All vertebrates in
the ingroup have a
backbone which is
a shared primitive
character present
in an ancestral
vertebrate but not
the outgroup.
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Outgroup Comparison
Going back to the
lancet, the lancet
is in the outgroup
and doesn’t have a
backbone.
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Outgroup Comparison
For example, let’s look at hinged jaws.
These are absent in lampreys, but are
found in other members of the ingroup-this represents a branch point.
The cladogram we’ve developed isn’t a
phylogenetic tree, we need more
information from fossils, etc. to indicate
when the groups first appeared.
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How Do We Build a Tree?
Maximum parsimony is the way in
which we look at our tree to ensure it is
consistent with the facts.
Maximum likelihood says that DNA
changes a certain way over time and
the tree built should reflect the likely
sequence of evolutionary events.
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A Question as an Example
What is the evolutionary relationship
between a human, a mushroom, and a
tulip?
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A Question as an Example
First we have to
look at the
molecular data.
Then we build the
tree that is
parsimonious and
likely.
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A Question as an Example
From this data,
we see that the
human and the
mushroom are
more closely
related than the
other two
scenarios.
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Tree 1 is Most Parsimonious
When building the trees, we assume
that the DNA is changing at equal rates
along all branches of the tree.
This makes Tree 1 more likely because
in Tree 2, the rate of evolution would
have had to slow in the human lineage
and speed up in the tulip lineage.
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Tree 1 is Most Parsimonious
Again, we assume that the DNA is
changing at equal rates along all
branches of the tree.
Tree 1 is again more likely because in
Tree 2, the rate of evolution would have
had to slow in the mushroom lineage
and speed up in the tulip lineage.
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Evolutionary History in the Genome
Much of the evolutionary history of an
organism can be seen looking through the
genome for differences.
Different genes often evolve at different rates,
even within the same evolutionary lineage.
Molecular trees have the ability to
encompass short and long periods of time
because genes evolve at different rates.
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Evolutionary History in the Genome
Example: Ribosome encoding DNA
The DNA that codes for rRNA evolves very
slowly and can be used to analyze the
relationships of organisms that diverged
millions of years ago.
Example: mtDNA
mtDNA evolves very quickly and is often
used to analyze more recent evolutionary
events.
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Molecular Clock
Making an estimate for how long ago a living
organism diverged from a common ancestor
requires the use of a molecular clock.
A molecular clock measures the absolute
time of evolutionary change based on the
observations that genes and other regions of
genomes evolve at seemingly constant rates.
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Molecular Clock
The main assumptions of the
molecular clock:
The number of substitutions in orthologous
genes is proportional to the time since the
species has branched from its common
ancestor.
For paralogous genes, the number of
substitutions are proportional to the time
since the genes were duplicated.
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Molecular Clock
As long as there are reliable rates of
evolution, we can calibrate the
molecular clock by graphing the number
of nucleotide differences against the
times of a series of evolutionary branch
points that are known from the fossil
record.
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Molecular Clock
The graph line created form this can then
be used to estimate evolutionary episodes
that can’t be discerned from the fossil
record.
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a. The volcanic origin of the Hawaiian islands has produced a chain of islands of increasing geological age. The
phylogenetic relationships of island endemic birds (for example, the drepananine (honeycreeper) species such as
the amakihi, Hemignathus virens and the akiapolaau Hemignathus wilsoni, shown in the tree) and fruitflies
(Drosophila spp.) reflect this volcanic 'conveyer belt', with the species of the oldest islands forming the deepest
branch of the tree, and the younger islands on the tips of the tree. Orange lines represent the outgroups. b.
Molecular dates for Hemignathus (panel b) confirm this order of colonization, and produce a remarkably linear
relationship between genetic divergence and time when DNA distance is plotted against island age. My, million
years. Figures from © (1998) Blackwell Publishing.
Molecular Clock
Although we can use the idea of a
molecular clock to estimate genes, age,
and behavior, some of them evolve at
different rates making estimation
difficult.
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Molecular Clock
There are many reasons for why molecular
clocks are not entirely accurate:
Changes in nucleotide sequences aren’t always
occurring at a constant rates and their effects
aren’t always neutral. Thus, differences in DNA
can evolve at different rates.
Differences in the rate of DNA evolution can also
make dating extremely old fossils difficult.
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