“ I checked it quite thoroughly,” said the
computer, “and that quite definitely is the
answer. I think the problem, to be quite
honest, is that you’ve never actually known
what the question is.”
Hitchhiker’s Guide to the Universe
Douglas Adams, 1979
Darwin’s
Notebook
“I think…
Thus between A and B
immense gap of
relation; C and B the
finest gradation, B and
D rather greater
distinction. Thus
genera would be
formed, bearing
relation…”
New title!
Phylogenetics and Systematics
Patrice Showers Corneli
Spring term 2010
“Case must be that [in]
one generation there
should be as many
living as now. To do
this and to have many
species in same genus
(as is) requires
extinction.”
Evolutionary Trees: Method,
Theory and Controversies
Patrice Showers Corneli
Spring term 2010
Tree from Origin of Species
Note bifurcating branches, extinctions, diversification
Useful terms for phylogenetic trees
Darwin’s trees
chimp
• Why did Darwin
join the taxa as he
did?
• What is the basis for
successively joining
taxa hierarchically
until they form a tree?
• What are the
implications for
evolution?
Equivalent cladograms for mammals
Aardvark
Dugong
Elephant
Procavia
Elephantus
Eshrew
Chrysochloris
Echinops
Alpaca
BlueWhale
FinWhale
SpermWhale
Hippo
Cow
Sheep
Pig
BlackBear
Grizzly
PolarBear
GraySeal
HarborSeal
Dog
Cat
Donkey
Horse
IndiaRhino
WhiteRhino
Chalinolobus
Pipistrellus
Rhinopholus
FruitBat
Pteropus
EuropeMole
Mogera
Urotrichus
Sorex
Soriculus
Echinosorex
Hedgehog
Hemiechinus
Baboon
Macaca
Chimp
Human
Gorilla
Orangutan
Gibbon
Cebus
Cynocephalus
Nycticebus
Tarsius
Dormouse
Squirrel
GuineaPig
Thryonomys
Mouse
Rat
Volemys
Pika
Rabbit
Tupaia
Armadillo
Anteater
Cladograms
Phylograms
arbitrary branch length
proportional length
chimp
human
human
gorilla
gorilla
orangutan
orangutan
Terminal nodes: taxa at end of branch
Internal node: circled branching point
Clade: a monophyletic group
Phylogram with the same taxa
Chrysochloris
Dugong
Elephant
Procavia
Elephantus
Eshrew
Echinops
Alpaca
Cow
Sheep
Pig
Cat
Donkey
Horse
IndiaRhino
WhiteRhino
Urotrichus
Sorex
Soriculus
Echinosorex
BlackBear
Grizzly
PolarBear
GraySeal
HarborSeal
Chalinolobus
Pipistrellus
Pika
Rabbit
Volemys
Elephant
Dugong
Echinops
Aardvark
Hemiechinus
Procavia
Mouse
Squirrel
Hedgehog
Chalinolobus
Pipistrellus
Chrysochloris
Rhinopholus
Echinosorex
Eshrew
Elephantus
Rat
Pteropus
FruitBat
Horse
Donkey
WhiteRhino
Dog
IndiaRhino
Anteater
Armadillo
BlackBear
Grizzly
Volemys
PolarBear
HarborSeal
Dormouse
Pig
Cat
GraySeal
Alpaca
Hedgehog
Hemiechinus
Cynocephalus
Nycticebus
Tarsius
Tupaia
BlueWhale
FinWhale
SpermWhale
Hippo
Dog
Rhinopholus
FruitBat
Pteropus
EuropeMole
Mogera
Phylogram
shows both
branching
order and
branch length.
Cladogenesis + Anagensis
(divergence pattern and
amount of evolution)
Equivalent phylogram: unrooted
Corneli, 2003
Aardvark
Corneli, 2003
Cladogenesis
(divergence pattern only)
Baboon
Macaca
Cebus
Gibbon
Gorilla
Orangutan
Thryonomys
Chimp
Human
SpermWhale
GuineaPig
Rabbit
Pika
Cynocephalus
Tupaia
Urotrichus
Sorex
Soriculus
Cow
EuropeMoleMogera
TarsiusNycticebus
Dormouse
Squirrel
GuineaPig
Thryonomys
Mouse
Rat
Baboon
Cebus
Macaca
Anteater
Armadillo
Gibbon
Orangutan
500 changes
Gorilla
Human
500 changes
Chimp
Sheep
Hippo
BlueWhale
FinWhale
Phylogenetic Trees
!
!
!
!
Example: How did domestic
dogs and wolves diverge?
Looking for pattern, humans
tend to group by similarities
Fully resolved hypothetical tree
Fully resolved hypothetical tree
Systematic way to visualize evolutionary history.
Not always interested in the tree itself.
Rather trees inform and constrain the set of
possible hypotheses about the biological
processes.
Examples
"
"
"
origins of mitochondrial DNA.
How do viruses (HIV) evolve? How can we fight them?
Why do unrelated badgers all look and act alike?
There are more than 2,000,000
possible trees for 9 dog breeds.
!
!
!
!
!
How can we infer the true tree?
Goal: Recover evolutionary history (trees).
Method: Separate similarity by descent
(homology) from similarity by convergence
(homoplasy).
Trees require homology.
Homoplasies can contradict the true
Each node
describes a
bifurcation
Common ancestor
Common ancestor
How do we get to full resolution?
What we know apriori
What we don’t know.
polytomy:
no phylogenetic information
one bifurcation
Common ancestor
Wolves and dogs share a common ancestor
Criteria for inferring branching?
shared derived
character:
floppy ears
Common Ancestor:
four legs, fierce face, erect ears, long ears
Criteria for inferring branching?
describes
another
bifurcation
shared derived
character:
floppy ears
Common Ancestor:
four legs, fierce face, erect ears, long ears
Another shared derived trait
now a total of 3
bifurcations
Two shared derived
characters:
floppy ears and
long ears
Cute eyes? Derived…
… but not shared.
cute eyes are derived
relative to the
common ancestor
Provides no phylogenetic information
cute eyes are derived
relative to the
common ancestor
four legs, fierce face, erect ears, long ears
Shared primitive trait: four legs
Another trait: body hair
Shared primitive character
Hairless dog
four legs, fierce face, erect ears, long ears
Common ancestor: body hair
Hairless dog
Common ancestor: body hair
Provides no phylogenetic information
Hairless dog
So similarity is necessary…
but not sufficient.
Phylogenetically useful traits:
shared and derived -> floppy ears, long ears
Phylogenetically useless traits:
shared primitive -> four legs, hair
derived but not shared -> cute eyes, hairless
retractable claws
no
ear flaps
abdominal
testes
short tail
Carnivorans: problem 9
retractable claws
no
ear flaps
Common Ancestor:long tail, ear flaps, external testes, fixed claws
no
ear flaps
abdominal
testes
short tail
Similarity alone: wrong tree
no
ear flaps
abdominal
testes
short tail
four shared derived
characters (synapomorphies)
retractable claws
Common Ancestor:long tail, ear flaps, external testes, fixed claws
Common ancestor: body hair
Carnivorans: problem 9
Carnivorans: problem 9
abdominal
testes
retractable claws
short tail
Note: highest similarity:
wolf and hyaena retain all
“primitive characters"
Common Ancestor:long tail, ear flaps, external testes, fixed claws
Note: highest similarity:
wolf and hyaena retain all
“primitive characters"
Common Ancestor:long tail, ear flaps, external testes, fixed claws
Phylogenetic groups
!
!
!
Monophyletic (or Natural) group
" An ancestor and all of its descendent taxa
" All taxa joined by shared derived character
(shared homology).
Paraphyletic group
" Taxa joined by shared primitive character
(retained homology).
Polyphyletic group
" Similarity by convergence (homoplasy).
!
Phenogram
"
!
"
"
!
!
!
!
Homology is a hypothesis of common
descent.
A character that is not supported by the tree
(i.e. lacks common ancestral state) exhibits
homoplasy.
Only homology corroborates a tree.
Homology of morphological, molecular,
behavioral or ecological characters
!
Taxa joined by similarity (apomorphy)
Cladogram
Joined by synapomorphy only
Arbitrary branch length
!
Phylogram
"
"
Homology vs. analogy
!
Homology vs. analogy
Types of phylogenetic trees
Hennig, 1965
Joined by synapomorphy only
Branch length depicts amount of evolution
These are our challenges.
!
!
!
!
To distinguish homology from homoplasy
To distinguish shared derived characters
(synapomorphies) from retained characters
(plesiomorphies).
Only synapomorphies are phylogenetically
informative.
Evolutionarily trees map synapomorphies.
!
Homology: shared ancestry of a character
" Bat wings and primate hands
" Human hair and cat hair
" Bird mtDNA and human mtDNA
Analogy: shared function of a character
" Bat wings and bird wings
" Insect and Vertebrate Eyes
Analogous characters are homplasies.
Next: tree quiz discussion
Next week:
Phylogenetic data: downloads and editing.
Numerical taxonomy and distance methods.
Simple models of evolution.