1. How do we infer phylogeny?
3 “schools” of phylogenetic thought:
Evolutionary systematics
Phenetics
Cladistics/phylogenetics

2. 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.

3. 1. Evolutionary systematics
-Often only classifications, with little attempt to depict
relationships as “trees” (phylogenies).
-”Trust the experts”

4. 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

5. 2. Phenetics: “phenograms”
Example from treeshrews. Implies RESEMBLANCE, *not* common ancestry.

6. 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

7. 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.
Defined on your handout.

8. 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).
All defined on your handout.

9. Bat Bird Pterosaur humerus humerus humerus
WINGS in tetrapods are not-homologous since they weren’t inherited from a common ancestor that possessed wings, but some of the individual elements ARE (e.g., humerus).
humerus
Pterosaur

10. Anapsida Diapsida Saurapsida Synapsida Amniota -ca. 320 mya
Lizards & snakes
Crocodiles
Dinosaurs & birds
Mammals &
reptile-like mammals
Turtles
Anapsida
Diapsida
Amphibians
Saurapsida
Synapsida
-ca. 320 mya
most recent common ancestor
Amniota
-evolution of cleidoic (shelled) egg;
ca. 350 mya

11. 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.
Defined on your handout.

12. 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.
Defined on your handout.

13. CHARACTER STATES are primitive or derived.
REMEMBER
CHARACTER STATES are primitive or derived.
ORGANISMS are not!
Think back to the platypus, echidna, ANY animal commonly referred to as “primitive”

14. Fossil record Ontogeny/embryology e.g., clavicles in deer
How do we identify “apomorphic” vs. “plesiomorphic”?
Fossil record
Ontogeny/embryology
e.g., clavicles in deer
Outgroup comparison
Example of outgroup comparison at end of lecture

15. 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.

16. Other criteria: Maximum likelihood; probabilistic
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).
Some people now distinguish b/w traditional “cladistics”, i.e. parsimony, and more statistically based methods like ML and Bayesian

17. 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).
Criterion: standard or measure by which something is selected. Plural is CRITERIA.
Some people now distinguish b/w traditional “cladistics”, i.e. parsimony, and more statistically based methods like ML and Bayesian

18. Ingroup taxa Number of trees 1 2 3 5 105 10 34,459,425 50
How many possible trees?
Ingroup taxa
Number of trees 1 2 3 5
105 10
34,459,425 50
x 1076
DON’T NEED TO REMEMBER THIS!!!!. By 100, greater than the estimated number of atoms in the universe!

19. Example Human Monkey Mouse Outgroup 1. Dense fur: no yes 2. Bipedal:
3. Computer:
4. Clothes:
5. Long tail:
6. Enlarged brain:
result is a CHARACTER MATRIX

20. “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