Today’s lecture
Understanding phylogenetic trees (part II)
Reconstructing phylogeny
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 reevaluation upon the discovery of new evidence.
How do we infer phylogeny?
Reconstructing phylogeny
From comparable similarities (characters); shared traits between species.
“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)
Charles Darwin photo by Leonard
Darwin, 1874. From Woodall, 1884:
Transactions of the Shropshire
Archaeological Society
Character/trait = a variable characteristic of an
organism, or group of organisms.
E.g. Body covering; flower color
yellow
white
feathers
scales
Character states = the different forms a character can take.
Reconstructing phylogeny: characters
Dial, 1992
Homology = homologous characters are
those inherited from a common ancestor.
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.
Reconstructing phylogeny: characters
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.
E.g., angiosperms (flowering plants)
Reconstructing phylogeny: characters
Ovules enclosed in carpels
Ovules enclosed in carpels:
synapomorphy
defining angiosperms
Soltis et al., 2011
Reconstructing phylogeny: characters
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.
E.g., “dicots”
vs. monocots
Reconstructing phylogeny: characters
One seed leaf
Two seed leaves:
symplesiomorphy
defining “dicots”
Reconstructing phylogeny: characters
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.
E.g., “Amentiferae”
Reconstructing phylogeny: characters
Wind pollination:
multiple origins
convergent characters
associated with wind pollination,
defining “Amentiferae”
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.
petals unfused
= ancestral
The preferred outgroup for
determining polarity is the
closest lineage to the
ingroup: the sister group.
Reconstructing phylogeny: in practice
Parsimony = the principle that the best explanation is the simplest one.
Trait a
Trait b
Taxon 1
Absent (0)
Present (1) Absent (0)
Taxon 2
Present (1) Absent (0)
Taxon 3
Present (1) Present (1) Present (1)
Outgroup
Absent (0)
1
2
3
a
4 steps
Absent (0)
out
1
Absent (0)
3
b
b
Present (1)
a, c = synapomorphies for 2+3
b = homoplasy (convergence)
Most parsimonious tree
out
Trait c
a
c
b
5 steps
2
c
a
c
out
1
2
b
a
3
c
b
6 steps
a
c
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