Understanding phylogenetic trees (part II)

Today’s lecture

Understanding phylogenetic trees (part II)

Phylogenetic inference = the process by which the branching pattern of evolutionary relationship (phylogeny) is estimated. A phylogenetic tree is a hypothesis; it is subject to re-evaluation upon the discovery of new evidence.

How do we infer phylogeny?

Reconstructing phylogeny

“The characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical.” Charles Darwin, On the Origin of Species (1859)

From comparable similarities (characters); shared traits between species.

Character/trait = a variable characteristic of an organism, or group of organisms.

Character states = the different forms a character can take.

Reconstructing phylogeny

Charles Darwin photo by Leonard Darwin, 1874. From Woodall, 1884: Transactions of the Shropshire Archaeological Society E.g. Body covering; flower color

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Homology = homologous characters are those inherited from a common ancestor.

Reconstructing phylogeny: characters

The states of homologous characters are comparable with one another, and may provide insight into evolutionary relationship.

Analogy = analogous characters have multiple, independent evolutionary origins.

Analogous characters do not provide useful indicators of evolutionary relationship.

Dial, 1992

Synapomorphy = shared, derived character. (from Greek: syn—together (shared) + apo—away + morph—form) A derived state shared by two or more lineages, which was present in their common ancestor, and is not found in other organisms.

Synapomorphies diagnose monophyletic groups.

Reconstructing phylogeny: characters

E.g., angiosperms (flowering plants)

Reconstructing phylogeny: characters

Ovules enclosed in carpels: synapomorphy

defining angiosperms

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Soltis et al., 2011

Symplesiomorphy = shared, ancestral character. (from Greek: syn—together (shared) + plesio—near + morph—form) An ancestral state shared by two or more lineages, which was present in their common ancestor, but is not found in all of its descendants. Symplesiomorphies diagnose paraphyletic groups.

Reconstructing phylogeny: characters

E.g., “dicots” vs. monocots

Reconstructing phylogeny: characters

Two seed leaves: symplesiomorphy

defining “dicots”

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Convergence or parallelism = analogy. (from Greek: homo—same + plassein—to mold) A state shared by two or more lineages which is not due to common ancestry. Convergent evolution, or parallelism. Convergent characters diagnose polyphyletic groups.

Reconstructing phylogeny: characters

E.g., “Amentiferae”

Reconstructing phylogeny: characters

convergent characters associated with wind pollination,

defining “Amentiferae”

Wind pollination: multiple origins

Reconstructing phylogeny: characters

Polarity = direction of evolutionary change.

How  do  we  know  what  is    ancestral  and  what  is    derived?  

Reconstructing phylogeny: characters

Polarity = direction of evolutionary change.

Polarity assessment

1) Fossil record – oldest is primitive

2) Simple to complex – evolutionary trends tend to reoccur in different groups

3) Correlation – primitive states tend to occur together in organisms

4) Common is primitive – “ingroup analysis”

5) Ontogeny – developmentally early stages are primitive

6) Outgroup comparison – inference from distribution of character states in sister group

Reconstructing phylogeny: characters

Polarity = direction of evolutionary change.

Outgroup comparison Character states in the outgroup = ancestral condition in the ingroup.

The preferred outgroup for determining polarity is the closest lineage to the ingroup: the sister group.

petals unfused = ancestral

out 1 2 3

4 steps

acb

b

out 1 23

5 steps

aa cc

b

out 1 32

6 steps

aa ccb

b

Parsimony = the principle that the best explanation is the simplest one.

Trait a Trait b Trait c Taxon 1 Absent (0) Present (1) Absent (0) Taxon 2 Present (1) Absent (0) Present (1) Taxon 3 Present (1) Present (1) Present (1) Outgroup Absent (0) Absent (0) Absent (0)

Most parsimonious tree a, c = synapomorphies for 2+3 b = homoplasy (convergence)

Reconstructing phylogeny: in practice

Real example with DNA sequence data (nucleotide characters).

Reconstructing phylogeny: in practice

In practice: many taxa, many characters; computationally intensive

Felsenstein,  1978  

Reconstructing phylogeny: in practice