Phylogenetic Analysis – Part 2

Spring 2013

Outline Why do we do phylogenetics

(cladistics)?

How do we build a tree?

Do we believe the tree?

Applications of phylogenetics (cladistics)

Why do we do phylogenetic analyses?

Evolutionary interpretation of relationships between organisms.

More reliable method of ascertaining the best hypothesis for how the organisms diverged from common ancestors.

Provides a better rationale for circumscribing taxonomic groups.

Enables testing of multiple hypotheses of relationships and character evolution based on specific character transformations.

Willi Hennig(1913-1976)

German Entomologist (Diptera)

Warren Herbert Wagner(1920-2000)

American Botanist (Pteridophytes,

Dendrogramaceae)

How do we build a tree? Data: Types of characters

Look for synapomorphies

Assemble the hierarchy of synapomorphies according to the principle of parsimony

Parsimony The idea that the simplest hypothesis is the

best explanation given the assumptions of the analysis.

Also known as Occam’s Razor In systematics, we look for the shortest trees

in any given phylogenetic analysis (maximum parsimony)…

…even though we know that evolution doesn’t necessarily proceed in a parsimonious manner.

Data: type of charactersCharacter Selection:

Must study each individual character to assure comparisons of homologous characters, and interpretation of the direction of character state transformations.

Some sources of characters: 1) morphology (external structure) or anatomy (internal

structure)

2) biochemical (photosynthetic pathway, pigmentation pathways, etc.)

3) chromosome numbers

4) nucleotide sequence data ( a t c g )

Character states Presence vs. absence (0 or 1): always binary

(two states) Other binary characters (0 or 1): yellow vs.

white flowers; range of measurements (quantitative)

Multi-state characters (3 or more states): e.g., yellow, white, or pink flowers or a t g c for nucleotide sequence data

For binary or multi-state characters, can hypothesize the direction of evolutionary change (transformation series)

Fig. 2.2

Pollen wall thickness µm (x axis)

Fig. 2.4 Examples of character state transformations

But how to hypothesize direction?

We usually have some working knowledge of the group under study (ingroup).

We choose a group thought to be closely related to the ingroup to serve as the outgroup as a basis of comparison.

Character states in the outgroup are assumed to be ancestral (plesiomorphic).

This allows us to establish the direction of character state transformation.

Phylogenetics or Cladistics

Bachia

Bachia

We need an outgroup, so wechoose the closely related genus Attigalea (there isevidence for this from otherstudies).

Cladistics

Attigalea

Bachia

Ingroup

Cladistics: characters

1. Leaf arrangement: alternate (0) or opposite (1)

2. Leaf midrib: white (0) or green (1)3. Leaf apex: rounded (0) or spiny (1)4. Sepals: present (0) or absent (1)5. Flower color: yellow (0) or blue (1)6. Subtending floral bracts: absent (0) or

present (1)

Cladistics: characters

1. Leaf arrangement: alternate (0) or opposite (1)

2. Leaf midrib: white (0) or green (1)3. Leaf apex: rounded (0) or spiny (1)4. Sepals: present (0) or absent (1)5. Flower color: yellow (0) or blue (1)6. Subtending floral bracts: absent (0) or

present (1)

Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0

Outgroup (Attigalea) Ingroup (Bachia)

Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0

Cladistics7 8 2 4 3 5 6 1

Leaves opposite

Sepals absent

Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0

Cladistics7 8 2 4 3 5 6 1

Leaves opposite

Sepals absent

Midrib green

Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0

Cladistics7 8 2 5 3 4 6 1

Leaves opposite

Sepals absent

Midrib green

Blue flowersFloral bractspresent

Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0

Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0

purple fringe

sepals absent

floral bractspresent

midrib green

Length = 5 steps

Attigalea Bachia

Cladistics: matrixCharacter 1 2 3 4 5 6Species 1 1 1 0 1 1 0Species 2 1 0 0 1 0 0Species 3 1 1 0 1 0 1Species 4 1 1 0 1 1 0Species 5 1 1 0 1 0 1Species 6 1 1 1 1 1 0Species 7 0 0 0 0 0 0Species 8 0 0 1 0 0 0

Homoplasy?Polymorphism in the outgroup

purple fringe

sepals absent

floral bractspresent

midrib green

spiny leaftip

spiny leaf tip

Length = 7 steps

Attigalea Bachia

Do we believe the tree? Various programs to generate trees. Various measures of statistical support

for the clades and for the characters. Can quantify the effects of homoplasy. Can test alternate arrangements to

examine the number of steps involved.

purple fringe

sepals absent

floral bractspresent

midrib green

spiny leaftip

spiny leaf tip

Length = 10 steps (7 - 1 + 4)

Attigalea Bachia

Phylogenetic Methodology1. Selection of taxa to study - Individuals, populations,

species, etc. identified as the units of comparison. One or more related groups (outgroups) necessary to “root” the trees.

2. The units under study described for as many characters as possible for which homology can be demonstrated or reasonably assumed. Character states assigned based on variation among the taxa in the ingroup and outgroup(s) and a priori hypotheses of the evolutionary direction of changes undergone by the character (character state polarization) are generated based on outgroup comparison.

3. A data matrix is assembled by scoring all taxa for all characters (ideally).

Phylogenetic Methodology(continued)

4. Using various analytical principles (maximum parsimony), a cladogram is constructed using synapomorphic character state changes to determine the tree topology. Systematists are seeking to define monophyletic groups (= clades).

5. Evaluation of the statistical confidence in how robustly the data support the grouping of organisms into clades is done next.

6. The subsequent grouping and ranking of the organisms in the resulting clades is then applied to classification systems or other questions.

Applications of phylogenetics

Classification

Biogeography

Many other possibilities (e.g., disease tracking, gene annotation)

Cladistics and Classification- Classifications based on tree topologies…Is it the best

tree? Will new data and new tree topologies necessitate complete overhaul of classification?

- Remember, systematists would like to define and name monophyletic groups (clades). Is this always possible? Must we accept paraphyletic groups?

- Classifications must also be useful for communication. Do the groups truly represent the best evolutionary hypothesis, and yet are the classifications useful?

Phylogenetics and Classification

Phylogenetics and Classification

Fig. 2.19A-C

Adansonia(baobab tree)

(Judd et al. 2008)

Phylogenetics and Biogeography

Fig. 2.22

Phylogenetics andCharacter Evolution

Fig. 19.11

Phylogenetics and ConservationAnomochloa

bamboo bluegrassBig bluestem

Northern sea oats

Grama grass