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 3. APweb 4. Gomez, 2010 5. Cameron, 2000
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Interpreting phylogenetic trees
Ingroup Outgroup Group 2 Group 1 H G F E D C B A Tip = extant species Terminal branch Node
Internal branch (internode) = ancestral species Root = common ancestor time
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
HomeothermiaHomeothermia (animals: thatan example are “warm of blooded”):a polyphyletic mammals group and birds
evolution.berkeley.edu Phylogenetic classification
Reptiles: flightlessReptiles, animals dinosaurs: with keratin examples scales Birdsof 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 re- evaluation upon the discovery of new evidence.
How do we infer phylogeny? Reconstructing phylogeny
From comparable similarities (characters); shared traits between species.