Today’s lecture
Understanding phylogenetic trees
Phylogeny = the pattern of evolutionary relationships among species, their descent from common ancestors
What is phylogeny?
“… 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)
Haeckel, 1866 Haeckel, 1874 Heinrich Bronn, 1858 Augustin Augier, 1801
Phylogeny is often presented as a diagram (a phylogenetic tree).
What is phylogeny?
1. Haeckel, 1866 2. Wikipedia 3. APweb 4. Gomez, 2010 5. Cameron, 2000
1
2
3
4
5
Node
H G F E D C B A Terminal branch
Internal branch (internode) = ancestral species
Root = common ancestor
Group 1 Group 2 Outgroup Ingroup
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.
time
Interpreting phylogenetic trees
Tip = extant species
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).
Topology = the branching pattern of a phylogenetic tree
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
Interpreting phylogenetic trees
Paraphyletic group = a group containing a common ancestor and some, but not all, of its descendants.
para = near, �not quite�, phylum = tribe
H G F E D C B A
Interpreting phylogenetic trees
Polyphyletic group = multiple lineages; a group that does not contain the common ancestor of its members.
poly = many, phylum = tribe
Phylogenetic classification = a hierarchical ordering of taxa, according to phylogenetic relationships. Our goal is to recognize and name only monophyletic groups, to achieve nested sets that are hierarchically organized.
Phylogenetic classification
The use of phylogeny to produce the classification. Often referred to as cladistics.
Chordates Amniotes
Mammals
evolution.berkeley.edu
Phylogenetic classification
Homeothermia (animals that are “warm blooded”): mammals and birds Homeothermia: an example of a polyphyletic group
biology.unm.edu
Phylogenetic classification
Reptiles: flightless animals with keratin scales Birds: flying animals with keratin feathers Reptiles, dinosaurs: examples of paraphyletic groups
xkcd.com(
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
Before: Chamaecyparis nootkatensis
Taxonomic revision
Gadek et al., 2000
Alaska yellow cedar
Xanthocyparis vietnamensis
Taxonomic revision
Before: Chamaecyparis nootkatensis
Farjon et al., 2002
Alaska yellow cedar
Now: Xanthocyparis nootkatensis
Before: Lycopersicon esculentum
Spooner et al., 1993
Taxonomic revision
tomato
Now: Solanum lycopersicum
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 Eg. Body covering; flower color
scal
es
feat
hers
whi
te
yello
w
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
Ovu
les
encl
osed
in c
arpe
ls
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”
One
see
d le
af
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.
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.
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)
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).
Reconstructing phylogeny: in practice