Table of Contents
-
Distance Methods
-
Some common models of sequence
evolution used in distance analysis:
-
Jukes and Cantor Model
-
The Natural Logarithm is used
to correct for superimposed changes at the same site
-
A four taxon problem for Deinococcus
and Thermus (Thermus, Deinococcus, Bacillus, Aquifex)
-
Comparison of P distances and
JC distances
-
The 16S rRNA genes of Aquifex,
Bacillus, Deinococcus and Thermus
-
Distance models can be made
more parameter rich to increase their realism 1
-
Distance models can be made
more parameter rich to increase their realism 2
-
The logDet/paralinear distances
method
-
LogDet / Paralinear distances
method
-
LogDet - a worked example for
two sequences A and B
-
The logDet/paralinear distances
method can find the true tree for Deinococcus + Thermus
-
The logDet/paralinear distances
method: advantages
-
Distances: advantages:
-
Distances: disadvantages:
-
Site-Rate Heterogeneity can
be a big Problem for Phylogenetic Analysis 1
-
Site-Rate Heterogeneity can
be a big Problem for Phylogenetic Analysis 2
-
What is the First Branch in
the Eukaryote Tree? - Microsporidia?
-
Microsporidia have a number
of unusual features
-
Alternative explanations of
Microsporidia unusual features
-
Some inventions in eukaryote
evolution?
-
Maximum likelihood protein tree
for Elongation factor 2
-
One can reduce site-rate heterogeneity
by editing data or including a site rate correction
-
ML tree for EF-2 sequences in
the absence of outgroups and with fast-evolving sites removed
-
LogDet tree from variable sites
(DNA, positions 1+2) for EF-2
-
Effect of CSR and outgroup choice
on Bootstrap support in LogDet analyses of EF-2 (DNA, positions 1+2)
-
Some inventions in eukaryote
evolution?
-
Summary - Microsporidia are
related to fungi
-
Obtaining a tree using pairwise
distances
-
Obtaining a tree using pairwise
distances
-
An perfectly additive tree
-
Obtaining a tree using pairwise
distances
-
Distance estimates may not make
an additive tree
-
Numbers of possible trees for
N taxa:
-
Obtaining a tree using pairwise
distances
-
Fitch Margoliash Method 1968:
-
Fitch Margoliash Method 1968:
an example
-
Minimum
Evolution method: an example
|
Author:
Martin Embley
Email: tme@nhm.ac.uk
Home Page: http://www.nhm.ac.uk/zoology/home/embley.htm |