Today’s lecture
Understanding phylogenetic trees
What is phylogeny?
Phylogeny = the pattern of evolutionary relationships
among species, their descent from common ancestors
“… the great Tree of Life, which fills with its dead and broken branches
the crust of the earth, and covers the surface with its ever-branching and
beautiful ramifications.”
Charles Darwin, On the Origin of Species (1859)
Augustin Augier, 1801
Heinrich Bronn, 1858
Haeckel, 1866
Haeckel, 1874
What is phylogeny?
Phylogeny is often presented as a diagram (a phylogenetic tree).
1. Haeckel, 1866
2. Wikipedia
3. APweb
4. Gomez, 2010
5. Cameron, 2000
3
4
1
5
2
Interpreting phylogenetic trees
Outgroup
H
G
Ingroup
Group 2
Group 1
F E D C
B
A
Tip = extant species
Terminal branch
Node
time
Internal branch (internode)
= ancestral species
Root = common ancestor
Ingroup = the lineage under consideration. Outgroup = a lineage that is not
part of the ingroup.
Sister group = the lineage that is most closely related to the lineage under
consideration.
Interpreting phylogenetic trees
Topology = the branching pattern of a phylogenetic tree
Sister relationships are reciprocal; sister groups are each other’s
closest relatives (share a more recent common ancestor with
each other than with any other group).
Interpreting phylogenetic trees
H
G
F E D
C
B
A
Monophyletic group (or clade) = a single lineage; a group
composed of a common ancestor and all of its descendants.
mono = one, phylum = tribe
Interpreting phylogenetic trees
H
G
F E D
C
B
A
Paraphyletic group = a group containing a common
ancestor and some, but not all, of its descendants.
para = near, not quite , phylum = tribe
Interpreting phylogenetic trees
H
G
F E D
C
B
A
Polyphyletic group = multiple lineages; a group that does
not contain the common ancestor of its members.
poly = many, phylum = tribe
Phylogenetic classification
Phylogenetic classification = a hierarchical ordering of taxa,
according to phylogenetic relationships.
The use of phylogeny to produce the classification.
Often referred to as cladistics.
Our goal is to recognize and name only monophyletic groups,
to achieve nested sets that are hierarchically organized.
Chordates
Amniotes
Mammals
Phylogenetic classification
Homeothermia
(animals that
are “warm
mammals
Homeothermia:
an example
of blooded”):
a polyphyletic
group and birds
evolution.berkeley.edu
Phylogenetic classification
Reptiles: flightless
Reptiles,
animalsdinosaurs:
with keratin
examples
scales Birds:
of paraphyletic
flying animals
groups
with keratin feathers
biology.unm.edu
Phylogenetic classification
Why no polyphyletic groups?
–  Natural classification should
reflect evolutionary relationship
Why no paraphyletic groups?
–  Taxa at same rank should not
contain one another
–  All members of a group should
have their closest relative also
belong to that group
Recognizing monophyletic groups
allows greater predictive power
xkcd.com(
Taxonomic revision
Gadek et al., 2000
Alaska
yellow cedar
Before:
Chamaecyparis
nootkatensis
Xanthocyparis vietnamensis
Taxonomic revision
Farjon et al., 2002
Alaska
yellow cedar
Before:
Chamaecyparis
nootkatensis
Now:
Xanthocyparis
nootkatensis
Taxonomic revision
tomato
Before:
Lycopersicon esculentum
Now:
Solanum lycopersicum
Spooner et al., 1993
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.
Eg. 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
Homoplasy = convergent character, 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.
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.
out
1
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)
2
3
1
a
b
5 steps
Absent (0)
3
a
c
Present (1)
Absent (0)
b
b
4 steps
out
Trait c
2
c
a
c
out
1
2
b
a
3
c
b
6 steps
a
c
Reconstructing phylogeny: in practice
In practice: many taxa, many characters; computationally intensive
Felsenstein,(1978(
Reconstructing phylogeny: in practice
Real example with DNA
sequence data (nucleotide
characters).