synapomorphy Principles of Phylogenetics: Tree Thinking PHYLOGENETIC INFERENCE PHYLOGENETIC INFERENCE Goal: Principles: PHYLOGENETIC INFERENCE

Principles of Phylogenetics: Tree Thinking Tree-speak tip tip tip tip branch branch Yes No node Wings PHYLOGENETIC INFERENCE PHYLOGENETIC IN...
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Principles of Phylogenetics: Tree Thinking

Tree-speak tip

tip

tip

tip

branch branch Yes

No

node

Wings

PHYLOGENETIC INFERENCE

PHYLOGENETIC INFERENCE

Goal:

Principles:

Seeks to recover the genealogical patterns of relationships among organisms

PHYLOGENETIC INFERENCE Principles:

1. Assumes similar features (characters) are homologous until shown otherwise

synapomorphy shared

derived

character

Assumes similar features are homologous until shown otherwise 2. Uses shared derived features, not shared ancestral features (Hennig formalized this)

Australopithecus

Homo

Large braincases Willi Hennig (1950s-1960s)

1

autapomorphy uniquely

derived

Australopithecus

character

H. sapiens

symplesiomorphy shared

ancestral

Australopithecus

character

Homo

High forehead bipedal

PHYLOGENETIC INFERENCE

PHYLOGENETIC INFERENCE

Principles:

Principles:

Assumes similar features are homologous until shown otherwise

Assumes similar features are homologous until shown otherwise

Uses shared derived features, not shared ancestral ones (Hennig formalized this)

Uses shared derived features, not shared ancestral ones (Hennig formalized this)

3. Treats shared derived features (character states) as markers of historical relatedness

Treats shared derived features (character states) as markers of historical relatedness 4. Same basic logic used for comparative morphology or DNA

A simple example….. TANAGER

TREE FROG

internal skeleton wings 2 legs feathers “warm-blooded”

internal skeleton no wings 4 legs no hair or feathers “cold-blooded”

BUMBLE BEE

OPOSSUM

external skeleton wings 6 legs hair “cold-blooded”

Internal skeleton no wings 4 legs hair “warm-blooded”

First taking one character at a time….

Character State

Character State

External (0)

Skeleton

Internal (1)

Character

2

First taking one character at a time….

(1)

(0)

(1)

(1)

Yes

No

Internal

External

Wings

Skeleton

bird wings are homologous to front legs of frogs and opossum. and NOT to wings of bee

Yes, but convergent

But….

No

Wings

so…

2

4

Legs

bird wings are homologous to front legs of frogs and opossum. so birds have 4 legs!

6

But….

so…

3

4

Poikilothermic (“cold-blooded”)

6

metabolism

Legs

really….

Endothermic (“warm-blooded”)

(actually bumble bees can be endothermic temporarily…)

Is hair of opossum and bee really homologous?

Just skin

Hair

Feathers

Hair

Body covering

But….

How can we combine the information from different characters to infer an overall phylogeny?

Character state trees

External

Internal

Yes, but convergent

No

Wings

Skeleton

4

We can test whether these groups share common ancestry using other characters….

External

Internal

Skeleton

6

Endothermic (“warm-blooded”)

Metabolism

No

Wings

4

Legs

Poikilothermic (“cold-blooded”)

Yes, but convergent

6

Legs

Just skin Feathers

Hair

Body covering

Poikilothermic (“cold-blooded”)

Endothermic (“warm-blooded”)

Metabolism

Just skin Feathers

Hair

Body covering

4

How can we combine the information from different characters to infer an overall phylogeny? If for only a few characters with no conflict, you can do this in your head, but if there is conflict quantitative methods are now implemented by computer to do this!

How do we know which state of a character is the ancestral one and which is derived?

First, make up a [character x taxon] matrix, converting ancestral states to 0’s and derived to 1’s or 2’s

Skeleton

Wings

Legs Metabolism Covering

Bumble bee

0

1

1

0

2

Tree frog

1

0

0

0

0

Tanager

1

2

0

1

1

Opossum

1

0

0

1

2

States found within the group of interest (ingroup) and also in related groups (outgroups) are more likely to be ancestral than those found only in the ingroup

-- Fossils may help show earlier appearance! -- Outgroup Comparison Considers that states found within the group of interest (ingroup) and also in related groups (outgroups) are more likely to be ancestral than those found only in the ingroup

endothermic poikilothermic outgroup ingroup

Skeleton

Wings

Legs Metabolism Covering

Bumble bee

0

1

1

0

2

Tree frog

1

0

0

0

0

Tanager

1

2

0

1

1

Opossum

1

0

0

1

2

Poikilothermy is likely to be ancestral

These are then “optimized” onto possible phylogenetic trees, and the tree that requires the fewest total changes of character state is chosen as the most likely (basic maximum parsimony analysis)

(It is also possible to make decisions among trees based upon the likelihood of alternative changes, rather than simply the evolutionarily “shortest” tree (we’ll see this with molecular data)

5

Using only the derived states….! How do we resolve differences in relationships implied by different characters (character state conflict)?

1

2 1

1

1 1 skeleton

2

2

Skel Wing Leg Metab Cov Bumble bee 0 1 2 1 0 Tree frog

1

0

0

0

0

Tanager

1

2

0

1

1

Opossum

1

0

0

1

2

legs metabolism

wings

Poikilothermic (“cold-blooded”)

Endothermic (“warm-blooded”)

Just skin

Feathers

Hair

Body covering

Metabolism

covering

Using only the derived states….!

This tree requires 8 steps, including an extra step (homoplasy) due to convergence in covering character

How many steps or evolutionary changes result from mapping the different character states onto these two other tree topologies?

1 2 2

1

1

Using the principle of maximum parsimony, which tree would be selected as the more likely ?

2

1 1

8 steps

1

2

2

Skel Wing Leg Metab Cover Bumble bee 0 1 1 0 2 Tree frog 1 0 0 0 0

1

1 1 skeleton

wings

steps

steps

2

1

legs metabolism

covering

Tanager

1

2

0

1

Opossum

1

0

0

1

1 2

Terms systematics [taxonomy, phylogenetics] phylogeny/phylogenetic tree cladogram tips, branches, nodes homology apomorphy synapomorhy autapomorphy plesiomorphy symplesiomorphy homoplasy convergence reversal of trait

monophyletic paraphyletic polyphyletic tree polarity outgroup ancestral group sister group character congruence topological congruence maximum parsimony

Willi Hennig

6

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