Tree thinking
Evolutionary History
Phylogeny
What is a phylogeny?
Branching diagram showing relationships between species (or higher taxa)
based on their shared common ancestors
Species: A
B
C
D
Time
E
F
A and B are most closely related because they share a common ancestor
( call the ancestor “E”) that C and D do not share
A+B+C are more closely related to each other than to D because they share
a common ancestor (“F”) that D does not share
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Morphological characters
Examples
Skull structure in cetaceans
Genitalia in ants
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Phylogeny
Outgroup
Species A
Species B
Species C
AAGCTTCATAGGAGCAACCATTCTAATAATAAGCCTCATAAAGCC
AAGCTTCACCGGCGCAGTTATCCTCATAATATGCCTCATAATGCC
GTGCTTCACCGACGCAGTTGTCCTCATAATGTGCCTCACTATGCC
GTGCTTCACCGACGCAGTTGCCCTCATGATGAGCCTCACTATGCA
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Phylogenetics
Sequences compared to evaluate
homology
• Different rates of change, esp. among
protein types
– Depends on protein function and
contribution to fitness
• Different rates even within a molecule
– 16S rRNA: conserved and variable regions
– Proteins: conserved domains, variable
loops
• Different rates between proteins and
between RNAs (and within molecules),
based on function and fitness.
Tree of life
Why is phylogeny important?
Understanding and classifying the
diversity of life on Earth
Testing evolutionary hypotheses:
- trait evolution
- coevolution
- mode and pattern of speciation
- correlated trait evolution
- biogeography
- geographic origins
- age of different taxa
- nature of molecular evolution
- disease epidemiology
- forensics – crime solving
…and many more applications!
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Phylogeny
Terminal nodes = contemporary taxa
Internal nodes =
ancestral taxa
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On a species phylogeny a node indicates a
speciation event
Evolutionary History
Phylogenetics
• Homology
http://www.swbic.org/education/bioinfo/molphylo.html
Phylogeny and classification
Monophyletic group
Paraphyletic group
Polyphyletic group
Includes an ancestor
all of its descendants
Includes ancestor and
some, but not all of its
descendants
Includes two convergent
descendants but not their
common ancestor
A
B
C
D
How could this happen?
A
B
C
D
Taxon A is highly derived
and looks very different
from B, C, and ancestor
A
B
C
D
Taxon A and C share
similar traits through
convergent evolution
Only monophyletic groups (clades) are recognized in cladistic classification
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Phylogeny and classification
Monophyly
Each of the colored lineages
in this echinoderm phylogeny
is a good monophyletic group
Asteroidea
Ophiuroidea
Echinoidea
Holothuroidea
Crinoidea
Each group shares a common
ancestor that is not shared by any
members of another group
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Phylogeny and classification
Monophyletic group
Paraphyletic group
Polyphyletic group
Includes an ancestor
all of its descendants
Includes ancestor and
some, but not all of its
descendants
Includes two convergent
descendants but not their
common ancestor
A
B
C
D
How could this happen?
A
B
C
D
Taxon A is highly derived
and looks very different
from B, C, and ancestor
A
B
C
D
Taxon A and C share
similar traits through
convergent evolution
Only monophyletic groups (clades) are recognized in cladistic classification
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Paraphyletic groups
Foxes
Paraphyly
“Foxes” are paraphyletic with respect
to dogs, wolves, jackals, coyotes, etc.
This is a trivial example because
“fox” and “dog” are not formal
taxonomic units, but it does show
that a dog or a wolf is just a derived
fox in the phylogenetic sense
Lindblad-Toh et al. (2005) Nature 438: 803-819
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Phylogeny and classification
Monophyletic group
Paraphyletic group
Polyphyletic group
Includes an ancestor
all of its descendants
Includes ancestor and
some, but not all of its
descendants
Includes two convergent
descendants but not their
common ancestor
A
B
C
D
How could this happen?
A
B
C
D
Taxon A is highly derived
and looks very different
from B, C, and ancestor
A
B
C
D
Taxon A and C share
similar traits through
convergent evolution
Only monophyletic groups (clades) are recognized in cladistic classification
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Paraphyletic groups
Lizards
Paraphyly
“Lizards” (Sauria) are
paraphyletic with respect
to snakes (Serpentes)
Serpentes is a monophyletic
clade within lizards
Squamata (lizards + snakes)
is a monophyletic clade
sister to sphenodontida
Snakes are just derived,
limbless lizards
Fry et al. (2006) Nature 439: 584-588
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Phylogenetics
Premise is that similarities among
structures in species derive from
vertical descent from common
ancestor.
•
Orthologs described by this
premise: homologs occurring in
different species.
– Usually with similar functions
•
Paralogs are homologs occurring
in same genome (same species).
– With different but often related
functions
Serb & Oakley 2005, Bioessays
Evolutionary History
Parsimony
How do we decide the “best” phylogeny?
Parsimony – the simplest explanation is preferred (Occam’s razor)
A trivial example (much more complicated with real datasets)
Most parsimonious:
Requires 5 steps
Requires only 4 steps
Round Î forked tail
Round Î forked tail
Round Î forked tail
Stripe Î barred
Spot Î plain tail
Stripe Î barred
Spot Î plain tail
No bump Î forehead bump
No bump Î forehead bump
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Consensus
When multiple phylogenies are supported…
A consensus tree shows only those relationships common to all trees
The lower tree is a “compromise” between conflicting upper phylogenies
Examples:
- two equally parsimonious trees
- two trees from different genes
- morphological vs. molecular tree
- parsimony vs. likelihood tree
Consensus trees will always have
at least one polytomy - a branching
event that is not a bifurcation
Better to have an incompletely resolved
tree than an incorrect tree
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Six Giraffe Species?
Approximate geographic ranges, pelage patterns, and phylogenetic
relationships between giraffe subspecies based on mtDNA sequences.
(From: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2254591/ )
(From: http://evolution.berkeley.edu/evolibrary/article/0_0_0/devitt_02 )
Cladogram of Ensatina
Phylogeny
Ensatina phylogeny based on mitochondrial DNA. Notice that oregonensis is composed of
four separate evolutionary lineages, which happen to be morphologically similar to one
another. Similarly, platensis is made up of two distinct lineages. In this case, Ensatina's
DNA reveals distinct evolutionary histories that morphology alone did not.
(From: http://evolution.berkeley.edu/evolibrary/article/0_0_0/devitt_03 )
Recognizing adaptations
•
The comparative method:
Recognizing adaptations
•
The comparative method: comparing sets of species to test
adaptation or other evolutionary phenomena
Nectarinia pulchella
Cyanerpes caeruleus
•
Vestiaria coccinea
Campylopterus hemileucurus
Phylogenetic relationships among taxa can ‘inflate’ observed
correlation of traits (samples not independent)
Y
Y
X
X
Speciation & Macroevolution
The Gradualism model
suggests that change is
gradual with the
accumulation of unique
morphological adaptation.
- The Punctuated
Equilibrium model
suggests that rapid change
occurs, with a new species
“erupting” from the
ancestral lineage and then
staying the same
thereafter.
Testing evolutionary hypotheses
Reconstructing ancestral characters
This phylogeny also shows how we can use
data from living species to infer character
states in ancestral taxa
?
?
Ancestral state could be blue, purple,
or intermediate…outgroup comparison
indicates blue is most parsimonious
Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644
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Testing evolutionary hypotheses
Mapping evolutionary transitions
Some horned lizards squirt blood from their eyes when attacked by canids
How many times has blood-squirting evolved?
Blood squirting?
No
Yes
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Testing evolutionary hypotheses
Mapping evolutionary transitions
Some horned lizards squirt blood from their eyes when attacked by canids
How many times has blood-squirting evolved? This phylogeny suggests a single
evolutionary gain and a single loss
of blood squirting
Blood squirting?
No
Yes
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Testing evolutionary hypotheses
Mapping evolutionary transitions
But a new phylogeny using multiple characters
suggests that blood squirting has been lost
many times in the evolution of this group
Our interpretation of these evolutionary
scenarios depends on phylogeny
Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644
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Testing evolutionary hypotheses
Convergence and modes of speciation
What can this phylogeny tell us about homology/analogy and speciation?
Lake Tanganyika
1.
Similarities between each pair are
the result of convergence
2.
Sympatric speciation more likely
than allopatric speciation
Lake Malawi
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Testing evolutionary hypotheses
Geographic origins
A
Where did domestic corn (Zea
mays maize) originate?
Populations from Highland Mexico
are at the base of each maize clade
B
Matsuoka et al. (2002)
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Testing evolutionary hypotheses
Geographic origins
Where did humans originate?
Each tip is one of 135 different
mitochondrial DNA types found
among 189 individual humans
African mtDNA types are clearly
basal on the tree, with the nonAfrican types derived
Suggests that humans originated in
Africa
Vigilant et al. (1991) Science
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