Outline
Character states
Evolutionary change on a tree Character data
• Evolutionary change on a tree
03‐327/727 Lecture 3
• Questions to ask with character state analysis
Fall 2012
• Characters and classification
• Molecular character data
• A character is a heritable trait or "well defined feature • A character is a heritable trait or "well defined feature
that … can assume one or more mutually exclusive that … can assume one or more mutually exclusive
states“* * Graur and Li, Molecular Evolution, 2000 states“* * Graur and Li, Molecular Evolution, 2000
• States can be • States can be
– binary (yes/no) or multistate (number of teeth) – binary (yes/no) or multistate (number of teeth)
– quantitative (weight) or qualitative (spotted) – quantitative (weight) or qualitative (spotted)
– discrete (number of legs) or continuous (weight) – discrete (number of legs) or continuous (weight)
Character: eye color Character states: blue, brown, green
mammary glands present, absent
Chimp Human Gorilla
number of legs 0, 2, 4, 6, 8, etc.
Fur Yes No Yes
Molecular
Weight (kg) 40-60 54-64 140-200
Characters nucleotide bases A, C, T, G
amino acids A, C, D, E, F, G, ….
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Morphological characters
Examples
Skull structure in cetaceans Genitalia in ants
Phylogeny of the Coleoptera Based on Morphological Characters of Adults and Larvae.
Lawrence et al. This is the result of scoring 359 beetle taxa for 516 morphological traits.
Evolutionary change on a tree
Outline
• Given
– a tree
• Character data
– a set of characters that are viariable for these taxa,
Evolutionary change on a tree – a character state matrix for the leaf taxa
• Questions to ask with character state analysis • infer
• Characters and classification – the character states of each ancestral node and
– the state changes along each branch
• Molecular character data • such the number of changes required is minimal
* Graur and Li, Molecular Evolution, 2000
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An example • Three changes
furry, light
• Two gains, one loss
gain: tool use
furry, light,
gain: tool use
body mass
loss: fur
Gorilla Chimp Human Gorilla Chimp Human
Fur Yes Yes No Fur Yes Yes No
Weight (kg) Heavy Light Light Weight (kg) Heavy Light Light
Tool use No Yes Yes Tool use No Yes Yes
A more complex example:
Character –State matrix Requires 4 steps
Character: Pattern Caudal Caudal Forehead
Pattern Shape Bulge?
Out
Round forked tail
Striped Spot Round No
A Synapomorphies
Barred None Forked No
Stripe barred
B
Spot plain tail
Barred None Forked No
No bump forehead bump
C
Barred None Round Yes
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Outline Questions to ask with character state analysis
• Character data • What were the properties of the ancestor?
• Evolutionary change on a tree • Which states are basal, which derived?
Questions to ask with character state analysis • Did certain character states arise more than once,
• Characters and classification independently (homoplasy, convergent evolution)?
• Molecular character data • Does the distribution of character states correlate
with other phenomena of interest?
• Basal states: furry, light
• Low body mass (~50kg) Questions to ask with character state analysis
• Fur
gain: tool use
• Derived states gain:
furry, light,
• Tool use
body mass
tool use
• What were the properties of the ancestor?
• High body mass (~175kg) loss: fur • Which states are basal, which derived?
• Did certain character states arise more than once,
independently (homoplasy, convergent evolution)?
• Does the distribution of character states correlate
Gorilla Chimp Human with other phenomena of interest?
Fur Yes Yes No
Weight (kg) Heavy Light Light
Tool use No Yes Yes
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Homoplasy Homoplasy
Taxa share a character, but not by descent from a common ancestor
Homoplasy is a product of convergent evolution Homoplasy is a product of convergent evolution:
Sabre‐toothed carnivores Taxa share a character, but not by descent from a common ancestor
M P
a l
r a
s c
u e
p n
i t Sabre tooth Wolf Sabre tooth Wolf
a a
l l
Marsupial Placental
Mapping evolutionary transitions: homoplasy Mapping evolutionary transitions: homoplasy
This phylogeny suggests a single evolutionary gain and two
lossesof blood squirting
Some horned lizards squirt
Blood squirting? No Yes
blood from their eyes when
attacked by canids
How many times has blood‐
squirting evolved?
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Reconstructing ancestral characters Mapping evolutionary transitions
The new phylogeny using multiple
characters suggests four
Color of internal nodes: independent losses of blood
Inferred ancestral horn length squirting behavior
Our interpretation of these evolutionary
scenarios depends on phylogeny
Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644 Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644
Mapping evolutionary Geographic origins
transitions
Where did domestic corn (Zea
mays maize) originate?
How many times has venom A Populations from Highland Mexico
are at the base of each maize clade
evolved in squamate reptiles?
Once in the large “venom clade”
Groups within this clade then
evolved different venom types B
e.g., different proteins found in
Snakes versus Gila monsters
Fry et al. (2006) Nature 439: 584‐588 Matsuoka et al. (2002)
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Geographic origins
Outline
Where did humans originate?
Each tip is one of 135 different
mitochondrial DNA types found
• Character data
among 189 individual humans • Evolutionary change on a tree
African mtDNA types are clearly
basal on the tree, with the non‐ • Questions to ask with character state analysis
African types derived
Characters and classification
Suggests that humans originated in
Africa • Molecular character data
Vigilant et al. (1991) Science
Classification: formal naming of groups of organisms Phenetics:
• Group organisms with similar properties
Formal naming of groups of organisms based on evolutionary relationships
• Does not reflect shared ancestry
Class Cladistics:
Order Order • Group organism with shared, derived character states (synapomorphies)
Family Family Family • Reflects shared ancestry
Genus Genus Genus Genus
Species 1 Species 1 Species 1 Species 1 Synapomorphy: Shared, derived character state (indicates homology)
Species 2 Species 2 Species 2 Species 2
Species 3 Species 3 Polarity: Distinguishing ancestral (0) from derived (1) = assigning polarity
Species 4 Species 4 Genus ‐ polarity can be assessed by outgroup comparison
Species 5 Species 1
Species 6 A B C D
Genus
Species 7
Species 1 Species 8 Genus
Species 2 Species 9 Species 1 “Red” is a synapomorphy for A + B
Species 3 Species 2
Species 3
“Circle” is a synapomorphy for A + B + C
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Phylogeny and classification Example: Deuterostomes are monophyletic
Monophyletic group
Includes an ancestor and all of its descendants
A B C D
Only monophyletic groups (clades) are recognized in cladistic classification The traits mapped onto
the phylogeny are
synapomorphies
Synapomorphy Convenience taxa:
named taxonomic groups that are not monophyletic
Paraphyletic group Polyphyletic group
How can we tell how well Includes ancestor and some, but not Includes two convergent descendants
a clade is supported? all of its descendants but not their common ancestor
In part, by the number of
synapomorphies A B C D A B C D
Few synapomorphies = weaker support
Many synapomorphies = stronger support
Taxon A is highly derived and looks Taxon A and C share similar traits
very different from B, C, and ancestor through convergent evolution
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Paraphyletic groups Paraphyletic groups
Foxes Canids
“Foxes” are paraphyletic with
respect to dogs, wolves, jackals, Note that canids are still a good
coyotes, etc. monophyletic clade within Mammalia
Each of the colored lineages within
canids is also a monophyletic clade
Lindblad-Toh et al. (2005) Nature 438: 803-819 Lindblad-Toh et al. (2005) Nature 438: 803-819
Paraphyletic groups Paraphyletic groups
Reptilia
Lizards “Lizards” (Sauria) are
paraphyletic with respect Birds are more closely related
to snakes (Serpentes) to crocodilians than to other
extant vertebrates
Serpentes is a monophyletic
clade within lizards
We think of reptiles as turtles,
Squamata (lizards + snakes) lizards, snakes, and crocodiles, but
is a monophyletic clade
reptilia is a paraphyletic
sister to sphenodontida
group unless it includes Aves
Snakes are just derived,
limbless lizards
Fry et al. (2006) Nature 439: 584-588
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Reconstructing evolutionary history Phylogeny and classification
Cladistic methods (Willi Hennig 1966)
Based on shared, derived characters = synapomorphies Classification Phylogeny
Similarity is not enough – requires similarity reflecting descent with modification Genus
Family
Requires characters that can be assigned a particular character state Genus
Order
Genus
Family
Genus
Class
Phylogenetic Classification
Genus
Phylogenetic (cladistic) classification reflects evolutionary history Family
Genus
The only objective form of classification – organisms share a true evolutionary Order
history regardless of our arbitrary decisions of how to classify them Genus
Family
Genus
Morphological characters
Outline
• Character data Character: Pattern Caudal Caudal Forehead
Pattern Shape Bulge?
• Evolutionary change on a tree Out
Striped Spot Round No
• Questions to ask with character state A
analysis Barred None Forked No
• Characters and classification B
Molecular character data Barred None Forked No
C
Barred None Round Yes
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Molecular characters Out: ACAGGTCG
A: GCACTTAG
Outgroup AAGCTTCATAGGAGCAACCATTCTAATAATAAGCCTCATAAAGCC B: GCACTTAG
Species A AAGCTTCACCGGCGCAGTTATCCTCATAATATGCCTCATAATGCC 3. Align
Species B GTGCTTCACCGACGCAGTTGTCCTCATAATGTGCCTCACTATGCC
C: GCAGTTCG
Species C GTGCTTCACCGACGCAGTTGCCCTCATGATGAGCCTCACTATGCA
Outgroup
Species A
2. Sequence
Species B
Species C
1. Extract
Out: ACAGGTCG Out: ACAGGTCG
A: GCACTTAG A: GCACTTAG
B: GCACTTAG B: GCACTTAG
C: GCAGTTCG C: GCAGTTCG
Outgroup Outgroup
Species A Species A G →C C →A
Species B Species B
A →G G →T
Species C Species C
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