understanding phylogenetic trees

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


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


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

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 = 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


Homeothermia (animals that are “warm blooded”): mammals and birds Homeothermia: an example of a polyphyletic group

biology.unm.edu


Reptiles: flightless animals with keratin scales Birds: flying animals with keratin feathers Reptiles, dinosaurs: examples of paraphyletic groups

xkcd.com(


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

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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.


E.g., angiosperms (flowering plants)


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.


E.g., “dicots” vs. monocots


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.


E.g., “Amentiferae”


convergent characters associated with wind pollination,

defining “Amentiferae”

Wind pollination: multiple origins


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(


Real example with DNA sequence data (nucleotide characters).


understanding phylogenetic trees

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