11/7/2013
The major points of this short section:
1. Trait evolution hypotheses must be
evaluated/tested
– Need a phylogeny
2. Phylogenies are hypotheses!
– Mo data mo betta
3. Taxonomy should reflect phylogeny!
– Names and ranks are meaningful
• You can build a hierarchical arrangement of
anything
• To recover the evolutionary history of
organisms we need a method that is
– Empirical
– Objective
– Testable
Darwin and Linnaean Classification
• Pre-Darwin Classification
• Post-Darwin Classification
Willi Hennig (1913-1976)
Phylogenetics
all true classification is genealogical; that community
of descent is the hidden bond which naturalists have
been unconsciously seeking, and not some unknown
plan of creation, or the enunciation of general
propositions, and the mere putting together and
separating objects more or less alike. – Charles Darwin
Phylogeny
• A phylogeny is a hypothesis of ancestordescendent relationships
• Usually shown as a cladogram
(C(P(R(W,H))))
1
11/7/2013
Phylogeny is genealogy
• Phylogeny is a genealogy writ large
Interpreting a phylogeny
•
•
•
•
•
•
Not a pedigree
• Pedigrees are reticulate
You spin me right round
Stratford, draw a sample
Tips are _______
Nodes are________
Branches are ______
A clade is _________
Traits are plotted _______
Phylogram
END DAY 1
2
11/7/2013
CHRONOGRAM
Phylograms: Quantifying differences
You’re like, in the outgroup
Higher organisms? – no way dude
• Organisms are
only more
ancestral or more
derived for a set of
characters
• Never use
“higher” or
“lower”
What to do with a phylogeny – opsis
case study
3
11/7/2013
Traits
•
•
•
•
•
•
•
•
•
Ancestral versus derived
Apomorphic
Plesiomorphic
Synapomorphy
Symplesiomorphy
Homologous verses analogous
Useful traits:
Not useful:
Misleading:
Assumptions of Phylogenetics
• organisms are related through descent
• lineages split (form sister species)
– How does this relate to synapomorphies?
• changes accumulate through time
– How does this relate to autapomorphies
• synapomorphies largely outnumber
homologies – traits that are shared between
organisms are there because of common
descent and not just similarity
OK… how do we make a phylogeny?
• Choose taxa
• Choose characters
– Resolution
– Not too fast, not too slow
• Determine polarity or select outgroup
• Group using synapomorphies
• Select method
– Parsimony
– Maximum likelihood
– Bayesian methods
• If testing a hypothesis of trait evolution map traits on
cladogram
END DAY 2
4
11/7/2013
To make a phylogenetic tree (review
and example)
• Choose characters and taxa
• Group by synapomorphies
Numbers of trees
Number of taxa / Number of trees (unique topologies)
• 5 15
• 6 105
• 7 945
(2t-3)! Over (2^(t-2) (t-2)!)
• 8 10,395
• 10 3 x 10^7
• 20 8 x 10^21
• 50 3 x 10^76
Potential to have multiple most parsimonious trees
Bootstrapping and Jackknifing
Resolving multiple parsimonious trees
• Leave it as a polytomy (strict consensus)
• Majority rule
Taxonomy and Phylogenetics
• Monophyly
• Paraphyly
• Polyphyly
Confidence in phylogenetic
hypotheses
• Robust phylogeny
• Congruence
– DNA
– RNA
– Behavior
– Geology
– parasites
5