Outgroups
Terminal node
(terminal)
(=interior branch)
“basal” to the ingroup
Most Recent Common
Ancestor of B+C
MRCA of A+B+C
MRCA of N+A+B+C
Monophyly
(monophyletic)
Paraphyly
(paraphyletic)
Polyphyly
(polyphyletic)
Monophyly
Non-monophyly
“... is more closely related to...”
=
“...shares a more recent common ancestor with...”
How do we infer phylogeny?
time
How do we infer phylogeny?
3 “schools” of phylogenetic thought:
1. Evolutionary systematics
1. Phenetics
1. Cladistics/phylogenetics
1. Evolutionary systematics
-Arose during the Modern Synthesis of Evolution
(Ernst Mayr, Theodosius Dobzhansky, G.G. Simpson)
1. Evolutionary systematics
-Arose during the Modern Synthesis of Evolution
(Ernst Mayr, Theodosius Dobzhansky, G.G. Simpson)
-Tried to be synonymous with evolutionary biology &
“Neo-Darwinism”
1. Evolutionary systematics
-Arose during the Modern Synthesis of Evolution
(Ernst Mayr, Theodosius Dobzhansky, G.G. Simpson)
-Tried to be synonymous with evolutionary biology &
“Neo-Darwinism”
-Goal: Think of relationships among organisms as how
Natural Selection made them.
1. Evolutionary systematics
-Arose during the Modern Synthesis of Evolution
(Ernst Mayr, Theodosius Dobzhansky, G.G. Simpson)
-Tried to be synonymous with evolutionary biology &
“Neo-Darwinism”
-Goal: Think of relationships among organisms as how
Natural Selection made them.
-Very little (if any) methodology or “operationalism”
Construct scenarios, but no formal system of theories.
1. Evolutionary systematics
-Arose during the Modern Synthesis of Evolution
(Ernst Mayr, Theodosius Dobzhansky, G.G. Simpson)
-Tried to be synonymous with evolutionary biology &
“Neo-Darwinism”
-Goal: Think of relationships among organisms as how
Natural Selection made them.
-Very little (if any) methodology or “operationalism”
Construct scenarios, but no formal system of theories.
-Difficult to formulate testable hypotheses.
1. Evolutionary systematics
-Often only classifications, with little attempt to depict
relationships as “trees” (phylogenies).
-”Trust the experts”
2. Phenetics
-Emphasizes the overall similarity of PHENOtypes
in grouping and classifying taxa.
2. Phenetics
-Emphasizes the overall similarity of PHENOtypes
in grouping and classifying taxa.
-Maintains principles of Neo-Darwinism, but
NO ESTIMATION OF PROCESSES (e.g., natural sel’n).
2. Phenetics
-Emphasizes the overall similarity of PHENOtypes
in grouping and classifying taxa.
-Maintains principles of Neo-Darwinism, but
NO ESTIMATION OF PROCESSES (e.g., natural sel’n).
-Largely methodological/operational.
NO PHILOSOPHICAL BASIS.
2. Phenetics
-Emphasizes the overall similarity of PHENOtypes
in grouping and classifying taxa.
-Maintains principles of Neo-Darwinism, but
NO ESTIMATION OF PROCESSES.
-Largely methodological/operational.
NO PHILOSOPHICAL BASIS.
-Uses any and all data, as long as it can be quantified.
2. Phenetics
-Emphasizes the overall similarity of PHENOtypes
in grouping and classifying taxa.
-Maintains principles of Neo-Darwinism, but
NO ESTIMATION OF PROCESSES.
-Largely methodological/operational.
NO PHILOSOPHICAL BASIS.
-Uses any and all data, as long as it can be quantified.
-Resulting “trees” called “Phenograms.” Statements of
SIMILARITY ONLY. Useful for summarizing
resemblence
2. Phenetics: “phenograms”
3. Cladistics/phylogenetics (Hennig)
3. Cladistics/phylogenetics (Hennig)
-Founded on principles of Operational Darwinism
3. Cladistics/phylogenetics (Hennig)
-Founded on principles of Operational Darwinism
1. Darwinian Evolution= “Descent with modification”
3. Cladistics/phylogenetics (Hennig)
-Founded on principles of Operational Darwinism
1. Darwinian Evolution= “Descent with modification”
2. Phylogeny is the result of evolution
3. Cladistics/phylogenetics (Hennig)
-Founded on principles of Operational Darwinism
1. Darwinian Evolution= “Descent with modification”
2. Phylogeny is the result of evolution
3. Therefore, focus on derived MODIFICATIONS
for evidence of phylogeny.
3. Cladistics/phylogenetics (Hennig)
-Founded on principles of Operational Darwinism
1. Darwinian Evolution= “Descent with modification”
2. Phylogeny is the result of evolution
3. Therefore, focus on derived MODIFICATIONS
for evidence of phylogeny.
-Cladistics uses ONLY shared,derived features to infer
phylogeny (Evolutionary Systematics & Phenetics use
ALL features).
3. Cladistics/phylogenetics (Hennig)
-Founded on principles of Operational Darwinism
1. Darwinian Evolution= “Descent with modification”
2. Phylogeny is the result of evolution
3. Therefore, focus on derived MODIFICATIONS
for evidence of phylogeny.
-Cladistics uses ONLY shared,derived features to infer
phylogeny (Evolutionary Systematics & Phenetics use
ALL features).
-Need to distinguish ANCESTRAL vs. DERIVED
Terms & concepts used in phylogenetics/cladistics
CHARACTER: Heritable trait possessed by an
organism; characters are usually described in
terms of their states, for example: "hair
present" vs. "hair absent," where "hair" is the
character, and "present" and "absent" are its
states.
Terms & concepts used in phylogenetics/cladistics
HOMOLOGY: Characters are considered homologous when they
are inherited from a common ancestor which possessed that
feature.
HOMOPLASY: A similar feature shared by two or more taxa that
does not meet the criterion (or criteria) of homology. Homoplasies
generally arise via convergence.
CONVERGENCE: the independent (convergent) evolution of
anatomical or functional similarity between unrelated or distantly
related lineages or forms. The resulting similarities are only
superficial, generally resulting from similar adaptation to similar
environments and are NOT a result of common ancestry (and are
therefore NOT homologies).
humerus
Bat
humerus
Bird
humerus
Pterosaur
Turtles
Anapsida
Lizards & snakes
Crocodiles
Dinosaurs & birds
Mammals &
reptile-like mammals
Diapsida
Amphibians
Saurapsida
Synapsida
-ca. 320 mya
most recent common ancestor
Amniota
-evolution of cleidoic (shelled) egg;
ca. 350 mya
Terms & concepts used in phylogenetics/cladistics
APOMORPHY: a derived feature or character; derived
from and differing from an ancestral (plesiomorphic)
condition.
SYNAPOMORPHY: A shared, derived character
(apomorphy) reflecting common ancestry used to group
taxa. Hair is a synapomorphy of mammals.
Terms & concepts used in phylogenetics/cladistics
PLESIOMORPHY: An ancestral or primitive character,
often incorrectly used to group taxa.
SYMPLESIOMORPHY: A plesiomorphy shared by two
or more taxa.
REMEMBER
CHARACTER STATES are primitive or
derived.
ORGANISMS are not!
How do we identify “apomorphic” vs. “plesiomorphic”?
How do we identify “apomorphic” vs. “plesiomorphic”?
1.Fossil record
How do we identify “apomorphic” vs. “plesiomorphic”?
1.Fossil record
2.Ontogeny/embryology
e.g., clavicles in deer
How do we identify “apomorphic” vs. “plesiomorphic”?
1.Fossil record
2.Ontogeny/embryology
e.g., clavicles in deer
3.Outgroup comparison
Parsimony Criterion
Parsimony Criterion
Parsimony: The “rule of simplicity.” Simply stated,
according to the principle of Maximum Parsimony,
accept the explanation requiring the fewest
assumptions.
Parsimony is the fundamental assumption of traditional
cladistics/phylogenetics.
Parsimony Criterion
Parsimony: The “rule of simplicity.” Simply stated,
according to the principle of Maximum Parsimony,
accept the explanation requiring the fewest
assumptions.
Parsimony is the fundamental assumption of traditional
cladistics/phylogenetics.
Other criteria: Maximum likelihood; probabilistic
criteria (e.g., Bayesian posterior probabilities).
Parsimony Criterion
In phylogenetics, we use the parsimony criterion to
“optimize” (=minimize) the number of transitions
(=steps) from one character state to another, for all
characters, on every possible tree, and select the tree
or trees that require the fewest number of steps (ad
hoc hypotheses).
We also use parsimony to infer character state
transformations and biogeographic history.
How many possible trees?
Ingroup taxa
Number of trees
1
1
How many possible trees?
Ingroup taxa
Number of trees
1
1
2
1
How many possible trees?
Ingroup taxa
Number of trees
1
1
2
1
3
3
How many possible trees?
Ingroup taxa
Number of trees
1
1
2
1
3
3
5
105
How many possible trees?
Ingroup taxa
Number of trees
1
1
2
1
3
3
5
105
10
34,459,425
How many possible trees?
Ingroup taxa
Number of trees
1
1
2
1
3
3
5
105
10
34,459,425
50
2.75292 x 1076
Example
Human
Monkey
Mouse
Outgroup
Example
1. Dense fur:
Human
Monkey
Mouse
Outgroup
no
yes
yes
yes
Example
Human
Monkey
Mouse
Outgroup
1. Dense fur:
no
yes
yes
yes
2. Bipedal:
yes
no
no
no
Example
Human
Monkey
Mouse
Outgroup
1. Dense fur:
no
yes
yes
yes
2. Bipedal:
yes
no
no
no
3. Computer:
yes
no
no
no
Example
Human
Monkey
Mouse
Outgroup
1. Dense fur:
no
yes
yes
yes
2. Bipedal:
yes
no
no
no
3. Computer:
yes
no
no
no
4. Clothes:
yes
no
no
no
Example
Human
Monkey
Mouse
Outgroup
1. Dense fur:
no
yes
yes
yes
2. Bipedal:
yes
no
no
no
3. Computer:
yes
no
no
no
4. Clothes:
yes
no
no
no
5. Long tail:
no
yes
yes
yes
Example
Human
Monkey
Mouse
Outgroup
1. Dense fur:
no
yes
yes
yes
2. Bipedal:
yes
no
no
no
3. Computer:
yes
no
no
no
4. Clothes:
yes
no
no
no
5. Long tail:
no
yes
yes
yes
6. Enlarged
brain:
yes
yes
no
no
Example
Human
Monkey
Mouse
Outgroup
1. Dense fur:
no
yes
yes
yes
2. Bipedal:
yes
no
no
no
3. Computer:
yes
no
no
no
4. Clothes:
yes
no
no
no
5. Long tail:
no
yes
yes
yes
6. Enlarged
brain:
yes
yes
no
no
Mammal Tree of Life (NSF): 4,500 morphological
characters and counting
“Nothing in biology makes sense except
in the light of evolution.”
T. Dobzhansky
“Nothing in biology makes sense except
in the light of evolution.”
T. Dobzhansky
“Nothing in evolution makes sense except
in the light of phylogeny.”
Society of Systematic Biologists