Transcript Chapter 25 Presentation

Chapter 25
Phylogeny and Systematics
The Fossil Record
The fossil record is an incomplete chronicle of
evolutionary time and change.
Most species that have ever lived did not die
in the right place at the right time to be
preserved in the fossil record.
Regardless, the fossil record is remarkably
detailed in its account of biological change
over geological time.
Morphology and Molecular
Similarities
In addition to the fossil record, scientists
also look at various morphological and
molecular similarities among living
organisms.
This helps them determine relatedness.
Homologies
Homologies are similarities due to a
shared ancestry.
Morphological homologies are shared
anatomical features which perform a
similar, basic function.
Genes and DNA can be homologous if
their similarities suggest they share a
common ancestor.
Hox genes.
Examining Phylogenies
When looking at phylogenies, it is
important to keep in mind the
differences between homologies and
analogies.
Homologies indicate a shared ancestry.
Analogies similarities in function due to
convergent evolution.
Convergent Evolution
Convergent evolution results when
similar environmental pressures and
natural selection produce similar
adaptations in organisms with different
evolutionary lineages.
Example: Australian and N. American
burrowing moles. Both occupy a similar
niche. However, one is a eutherian, the
other is a marsupial.
Phylogenetic Trees
Are branching diagrams that show how
organisms are related in the tree of life.
The shared characters of a phylogeny
are grouped into a branch of
dichotomous branching taxa. The
branches represent a divergence from a
common ancestor.
Phylogenetic Trees
Patterns of shared characters are depicted
in a cladogram. The cladogram doesn’t
necessarily represent an evolutionary
history, but if the homologies represent a
shared ancestry, then the cladogram forms
the basis of the phylogenetic tree.
A Clade
A clade is a group of species which
includes the ancestor and all of its
descendents.
The study of this is called cladistics.
Cladistics
Cladists seek to classify
all members of a
particular group of
organisms into a
particular branch on a
tree.
Ideally, the branch
includes all
descendents from a
common ancestor and
the ancestor--a
monophyletic clade.
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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
descendents.
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A Polyphyletic Clade
When we can group
a number of
organisms together
but can’t find their
common ancestor,
we have a
polyphyletic clade.
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The Distinction Between Homologous and
Analogous Similarities
It becomes difficult when you have to
sort through homologies to determine
shared primitive and shared derived
characters.
A shared primitive character is any
character that is shared beyond the
taxon we are trying to define.
Example: the backbone is the homologous
structure the predates the branching of the
mammalian clade from other vertebrate
clades.
The Distinction Between Homologous and
Analogous Similarities
A shared derived character is a evolutionary
novelty that is unique to a particular clade.
Example: Hair is a character shared by mammals,
but not found in non-mammalian vertebrates.
The backbone can qualify as a shared
derived character at a deeper branch point
that distinguishes all vertebrates from other
animals.
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.
Among eukaryotes it is a shared
derived character because it is an
evolutionary novelty that is unique to a
particular clade.
• A cladogram depitcs
patterns of shared
characteristics
between species.
Outgroups
To draw comparisons and differentiate
between shared derived characters and
shared primitive characters, scientists
use outgroups.
Outgroups comprise a species or group
of species that are closely related to the
group being studied, but not as closely
related as any study-group members
are to each other.
Outgroups
For example we’re
going to examine 5
vertebrates: a
leopard, a turtle, a
salamander, a tuna,
and a lamprey.
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.
Outgroup
The outgroup is less closely related than any
of the ingroup members are to each other
(based on the evidence).
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.
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.
Lancets have notochords their whole
life, vertebrates only have them during
embryonic development.
Outgroup Comparison
The species in the ingroup display 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.
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.
Going back to the lancet, the lancet is in
the outgroup and doesn’t have a
backbone.
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.
Phylograms and Ultrametric
Trees
The chronology of events in the evolutionary
history of the organism in study can be
represented using a phylogram or an
ultrametric tree.
Phylograms represent information about the
sequence of events relative to one another.
Ultrametric trees present information about
the actual time that given events occurred.
A Phylogram
The length of any
branch represents the
number of changes that
have taken place in a
particular DNA
sequence in that
lineage.
The longer the line, the
more changes that have
taken place since
divergence.
An Ultrametric Tree
The branching
pattern is similar to
that of a phylogram,
but all the branches
can be traced from a
common ancestor to
the present.
An Ultrametric Tree
The branching
pattern is based on
the data from the
fossil record, and is
placed in the context
of geological time.
Much of the evolutionary history of an
organism can be seen looking through
the genome for differences. Molecular
trees have the ability to encompass
short and long periods of time because
genes evolve at different rates.
Example: Ribosome encoding DNA
The DNA that codes for rRNA evolves very
slowly and can be used to analyze
organisms that are very old.
Example: mtDNA
mtDNA evolves very quickly and is often
used to analyze more recent evolutionary
events.
Gene Duplications
These are the most important evolutionary
events that increase the number of genes
within a genome.
They are also important from a phylogenetic
standpoint because they allow scientists to
examine genomes and look for duplications.
The information can then be used to show the
relatedness of the organisms to each other.
Orthologous Genes
These are genes which are passed on
in a straight line from one generation to
the next, but have ended up in the other
gene pools due to speciation--divergent
events.
Example: -hemoglobin in humans and
mice are orthologous.
Paralogous Genes
These genes result from gene
duplication, and more than one copy is
found within a genome.
Example: olfactory receptor genes have
undergone numerous gene duplications in
vertebrates.
Orthologous Vs. Paralogous
Of the two types of homologous genes,
only orthologous genes diverge after
speciation. Paralogous genes diverge
while they are in the same gene pool
because they are present in more than
one copy.
Orthologous Vs. Paralogous
Example: The orthologous gene for hemoglobin serves a similar function in
humans and mice, but their sequences
have diverged since their common
ancestor.
Orthologous Vs. Paralogous
Example: The paralogous genes
comprising the olfactory receptor
diverge while in the same gene pool
because there is more than one copy.
Our ability to identify a wide variety of
odors reflects this.
Genome Evolution
The commonality of orthologous genes
among a wide variety of organisms
demonstrates that all living organisms share
many biochemical and developmental
pathways.
Also, gene duplication has not kept up with
increasing phylogenetic complexity. The
versatility of our genes enables us to carry
out a wide variety of tasks as compared to
other organisms.
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.
Molecular Clock
The main assumptions of the
molecular clock:
1.
2.
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.
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.
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,c.
Molecular dates for Hemignathus (panel b) and Drosophila (panel c) 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.
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 make
dating extremely old fossils difficult.