CONSENSUS TREES
Loni Beaty
REVIEW


Phylogenetic Trees -> Figure depicting
evolutionary descent, communicating the
evolutionary relationship among entities
Important to know:


Phylogenetic trees may not represent the true
evolutionary history.
Why is this?
PROBLEMS WITH PHYLOGENIES

Why may a phylogenetic tree not actually be
correct?

Horizontal gene transfer


Hybridization


Acquiring the same or similar biological traits in unrelated
lineages
Conserved sequences


A process to measure the degree of genetic similarity
Convergent Evolution


Transfer of genetic material between organisms
Similar sequences occurring in RNA, DNA, protein
sequences, etc. across species.
More genes needed to be taken into account from
difference genomic sources
SO, WHAT DO WE USE THEN?

Consensus Trees:


A consensus tree is single evolutionary tree created
from a group of phylogenetic trees.
Why do we use these?

Life scientists can study this single consensus tree,
with the most robust branching patterns of the
phylogenetic tree of how the taxa evolved.
TREE SUPPORT

There are ways to express how good each
phylogenetic tree is.

Statistical Resampling
Resulting trees are pooled and presented on a majority
rule consensus tree.
 Nodes labeled with percentage of trees in which they
appear.
 Bootstrapping
 Resampling with replacement
 More common
 Jackknifing
 Resampling without replacement


Bremer Support (aka Decay Index)
BREMER SUPPORT

Difference in number of steps between the score
of trees and the score of the most parsimonious
tree not containing a particular clade.
A step is a change from one character state to
another, or evolutionary transition.
 The number of steps you have to add to lose a clade.
 Therefore, the larger the number, the stronger the
support for that node.


Decay indexes appear to be proportional to
bootstrap percentages.
BREMER SUPPORT IN PAUP
•Graph
depicts
relationship of 8
teleost fishes and
an outgroup.
•Optimal
tree is 82
steps long.
•If
run at 83 steps,
one step longer
that the optimal,
one ingroup
collapses to form a
trichotomy.
•If
run at 83 steps,
multiple ingroups
have collapsed.
•This
is continued
until the whole
tree is collapsed,
and each node has
a value.
•The
overall result
is the Decay
Index.
USE OF DATA

Dispute among cladists which is best:

Character Congruence


Combine all data into a large data set and analyze together
Taxonomic Congruence

Combine trees produced from different data
TYPES OF CONSENSUS TREES

There are quite a few types of consensus trees,
but the more prominent are:

Strict
evolutionary relationships that appear in all of the trees
 purists believe this is the only consensus method that
should be considered


Semi-strict
Combine all possible solutions that are not contradicted
 Sometimes called combinable component consensus


Majority Rule

branching patterns that exist in a majority of the trees
STRICT
•If
CONSENSUS TREES
the relationship
doesn’t appear on
ALL of the
phylogenetic trees,
it doesn’t appear
on the consensus
tree.
•Another
way of
looking at it is a
clade cannot be
confirmed unless
we’re sure of it.
SEMISTRICT CONSENSUS TREES
•So
long as no
trees are
contradicted by
other trees, it can
appear on the
consesus tree.
•Another
was to
look at it is, a
clade shouldn’t be
refused unless
there is a clear
contridiction.
MAJORITY RULE CONSENSUS TREES
•The
grouping only
has to be present
in the majority of
trees to be
represented in the
consensus tree.
•Majority
is
typically 50%.
•When
only
comparing two
trees, Strict
Consensus is used.
USEFUL PROGRAMS

PAUP – Phylogenetic Analysis Using Parsimony
Program for inferring evolutionary trees and
consensus trees
 Parsimony is character-based tree estimation
method.


TreeRot – program used to calculate the decay
index
REFERENCES




http://www.geol.umd.edu/~tholtz/G331/lectures/cladistics5.pdf
DEGNAN J, DEGIORGIO M, BRYANT D, ROSENBERG N.
Properties of Consensus Methods for Inferring Species Trees from
Gene Trees. Systematic Biology [serial online]. February
2009;58(1):35-54. Available from: Academic Search Complete,
Ipswich, MA. Accessed May 16, 2012.
http://www.sciencedirect.com.ezproxy.library.wwu.edu/science/art
icle/pii/S0025556410001227
Bioinformatics for Biologists text