Reconstructing Evolutionary
Trees
Chapter 14
Phylogenetic trees
The evolutionary history of a group of species = phylogeny
The problem:
Evolutionary histories can never truly be known.
Once again, we are using current day
patterns to reconstruct past processes.
We have an advantage since in some cases:
Because of fossils we also have insights into
past patterns.
The logic of phylogenetic
inference
The basic idea: Organisms that are similar in heritable
traits are related. The more similar, the more closely
related.
There
are lots of reasons we need to be careful
Organisms may be similar because of:
Common ancestry (homology) this is the interesting
one
it has “phylogenetic information”
Primitive characters (predates the evolution of the
group)
carries no phylogenetic signal.
Common environment (homoplasy, analogy)
carries no phylogenetic signal
Random events: reverse mutation can cause this
Shared Derived traits
The evolution of photosynthesis in algae
Synapomorphies
Synapomorphy: A shared, derived character; in a
phylogenetic analysis synapomorphies are used to
define clades and distinguish them from outgroups.
Shared Ancestral Traits?
QuickTime™ and a
GIF decompressor
are needed to see this picture.
Who is a reptile?
Shared Ancestral Traits
Tetrapods
Scales
“cold blooded”
Amniotic egg
Homoplasy
Sometimes Homoplasy is easy to detect.
Sometimes homoplasy is not
so easy
Is
photosynthesis
homoplasious?
Is “warm bloodedness”
homoplasious?
Birds
type 1
type 2
type 3a
type 3a+b
type 2
When did
complex
feathers
(3a+b)
arise?
Birds
Molecular data
Particularly serious problems arise with molecular data
Each “trait” (nucleotide) can take on only one of four states,
ATCG
ATTGCTATTC
ATTGCTATTC
Homoplas
y
mutation
ATTGCTTTTC
mutation
Molecular Data
Problem: there will always be
conflicts.
Good phylogenies are based on many traits, frequently
hundreds of traits may be used.
Some will have changes that are consistent, some won’t.
That is some traits will reflect homology, some will be
homoplasius.
How do we decide which are which?
Inferring process from pattern: We need rules.
Parsimony
We have run into parsimony before in group selection
Parsimony: The simplest explanation is the most likely to be
correct
In phylogenetic inference the “simplest” explanation is the tree
that requires the fewest evolutionary changes.
Because of back mutations, homoplasies etc. there will be
conflicts among traits in the “optimal” tree. Parsimony is the
idea that we minimize the number of changes across all traits.
In this example the tree is the same as Fig. 14.3, as is
yellow sequence.
In this set of sequences there must be at least one reversion.
TTTC
ATTGCG
ATTC ATTGCG
ATTC ATTGCG
TTTC ATTGCG
TGAATCC
GCC
TGAATCC GCC
CGAATCC GCC
TGAATCC GCC
TATAGTCAAT TATAATCAAT TATAATCAAT TATAATCAAT
ATTGCG
TTTC
GCC
CGAATCC
TATAATCAAT
GCCTGAATCC
GCCTGAATCC
GCCCGAATCC
GCCCGAATCC
ATTGCGATTC
TATAGTCAAT
ATTGCGTTTC
TATAATCAAT
These two trees are equally parsimonious (4 changes).
There is no way, using parsimony, to distinguish between
these two trees.
The answer as always: MORE DATA!
Outgroups
Phylogenetics is based on similarity of shared derived characte
Shared primitive characters do not contain information.
How do we determine what is derived and what is primitive?
The answer is to use an “outgroup”: A taxa that is closely
related but outside of (diverged before) the set of taxa
being analyzed.
Selection of appropriate outgroups can be difficult, and the
choice can change your answer.
Often multiple outgroups are used.
Which is better? Morphology
or Molecules
Answer is as usual: It depends.
Molecules:
Lots of data (base pairs)
Objective, but may be biased by available primers
Traits are mostly neutral (no ecological convergence)
Only 4 states (homoplasy common)
Morphology:
Usually less data
Subjective choice of trait states
Convergence due to ecological similarity an issue
Potentially many states, homoplasy less common
Example: Whales
The origin of whales was a major mystery as recently as 10
years ago.
The problem was: modern whales are so modified that tracing
their ancestry based on modern morphology is nearly
hopeless.
Two things broke this long standing mystery
(1) The recent discovery of fossil whales
(2) Modern molecular analysis.
Whale History
The ancestor of whales has been reasoned to be many things,
ranging from Carnivora to the more recently generally accepted
Artiodactyles
Astragalus Morphology
What should place Whales as Artiodactyles is the shape of the
Astragalus, an ankle bone that allows Artiodactyles to run
efficiently.
This bone is lost in modern whales!
Pulley
shaped
Astragalus
lost
Pulley
shaped
Astragalus
Parsimony favors this!
Pulley
shaped
Astragalus
Ambulocetus natans
Pulley shaped Astragalus
The Ambulocetus’s
astragallus tells us:
1. Whales are Artiodactyles
2. Whales had, but modern whales have lost, one of
the shared derived traits that distinguishes the
Artiodactyles.
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Dorudon
Basilosaurus
Molecular Data
The best analyses use both
molecular and morphological
data
For whales:
Morphology provides clear evidence in
the form of morphology (ankle bones)
that are unique to Artiodactyles
Molecular data: has the mass of data
to accurately place whales within the
Artiodactyle tree.
Finding the most parsimonius
tree can be problematical!
With more than a few taxa the number of possible trees
becomes enourmous.
With more than a few traits, finding the best fit tree is
VERY difficult.
Methods for finding the best tree is an extremely active
field of research, and there are a number of available
packages.
Approaches:
Maximum Likelihood
Bootstrapping
MC Markov Chain
MCMC -Markov Chain, Metropolis coupled methods
Why do we care?
We would like to group organisms into evolutionarily related set
Species: A set of interbreeding organisms
Genus: A set of species derived from a single ancestral specie
Family: A set of genera derived from a single ancestral specie
(In practice: drived from a single ancestral genus)
Etc.
This is cladistic view.
A raving cladist ONLY allows “monophyletic” groups
NEVER allows “polyphyletic” groups
NEVER allows “paraphyletic” groups
Types of groups
Monophyletic
Paraphyletic
Polyphyletic
Paraphyletic and polyphyletic are
very nearly the same thing.
Many groups are paraphyletic
“reptiles”
Should Paraphyletic groups
be “allowed”?
Some argue that they have no business being
considered scientifically valid groups
Others argue that such paraphyletic groups are
inevitable, and are not bad.
Question: Why are they “inevitable”?
Speciation by “Remote
Control”
A and A’ are two populations of the same species, A’ range
includes a cave. A group of A’ moves into the cave and
becomes species B. Are A and A’ different species?*
*I got this conundrum from Alan Templeton
What to do with phylogenies
Can we use phylogenetics and fossils to calibrate a
“molecular clock?
Why are certain species found in some regions of the world
and not others?
Do hosts and predators “cospeciate”?
Did unusual adaptations etc. evolve multiple times, or only
once?
Cospeciation
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Tanglegram showing host parasite associations between pocket
gophers and their chewing lice (modified from Hafner, M.S. &
Nadler, S.A. (1988) "Phylogenetic trees support the coevolution of
parasites and their hosts." Nature 332: 258-259)
Phylogenetically independent
comparisons
QuickTime™ and a
TIFF (LZW) decompressor
are needed to see this picture.
Is a trait homologous?
The Origins of AIDS
cpz = chimpanzee
monkeys
mnd = Mandrill
smm = sooty mangabee
syk = sykes monkeys
agm = African green
Phylogenetics & Disease
Control
The story revolves around Dr. David Acer, a Florida
dentist who died in 1990 from complications of AIDS.
Dr. Acer's death would have been far from remarkable
at the time -- the AIDS epidemic was quite visible by the
late 1980s, and one death earned no more attention
than any other. Dr. Acer's story, however, extends
beyond his private life and into his practice. You see, Dr.
Acer had multiple patients that had been diagnosed as
infected with HIV within a couple of years of his death.
Many of the infected patients showed no risk factors
associated with HIV infection. One elderly woman
(hardly the at risk type that Tara described) had been
married for more than 25 (her spouse was HIV
negative), had never used intravenous drugs, never had
sex with any at risk individuals, and never received a
blood transfusion. Another patient was not an
intravenous drug user, had no history of transfusion,
and all recent sexual contacts were HIV negative.
A phylogeny created using DNA sequences of the HIV
virus taken from the dentist, patients, and other
individuals within a 90 mile radius is shown below. Note
the cluster containing sequences from the Dentist,
Patient A, Patient B (the elderly woman), and Patient C
(the second patient described above).
Flu Phylogenies
Flu phylogenies show interference among
sublines. This is the effect of host immunity
Bird Flu H5N1
Show Google Earth here if possible.