Terminal node

(terminal)

(=interior branch)

Outgroups

Most Recent CommonAncestor of B+C

MRCA of A+B+C

MRCA of N+A+B+C

“basal” to the ingroup

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)

-Founded on principles of Operational Darwinism

3. Cladistics/phylogenetics (Hennig)

-Founded on principles of Operational Darwinism1. Darwinian Evolution= “Descent with modification”

3. Cladistics/phylogenetics (Hennig)

-Founded on principles of Operational Darwinism1. Darwinian Evolution= “Descent with modification”

2. Phylogeny is the result of evolution

3. Cladistics/phylogenetics (Hennig)

-Founded on principles of Operational Darwinism1. 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 Darwinism1. 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)

3. Cladistics/phylogenetics (Hennig)

-Founded on principles of Operational Darwinism1. 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.

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. Homoplasiesgenerally 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).

Terms & concepts used in phylogenetics/cladistics

Bat

Bird

Pterosaur

humerus

humerus

humerus

Anapsida Diapsida

SynapsidaSaurapsida

Turtles

Lizards & snakesCrocodilesDinosaurs & birds

Mammals &reptile-like mammals

Amniota -evolution of cleidoic (shelled) egg; ca. 350 mya

Amphibians

-ca. 320 mya

most recent common ancestor

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/embryologye.g., clavicles in deer

How do we identify “apomorphic” vs. “plesiomorphic”?

1.Fossil record

2.Ontogeny/embryologye.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; probabilisticcriteria (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 treeor 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 taxaNumber of trees

1 1

2 1

How many possible trees?

Ingroup taxaNumber of trees

1 1

2 1

3 3

How many possible trees?

Ingroup taxaNumber of trees

1 1

2 1

3 3

5 105

How many possible trees?

Ingroup taxaNumber of trees

1 1

2 1

3 3

5 105

10 34,459,425

How many possible trees?

Ingroup taxaNumber 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

Human Monkey Mouse Outgroup

1. Dense fur: 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 exceptin the light of evolution.”

T. Dobzhansky

“Nothing in biology makes sense exceptin the light of evolution.”

T. Dobzhansky

“Nothing in evolution makes sense exceptin the light of phylogeny.”

Society of Systematic Biologists