Glossary of terms used in Phylogeny Reconstruction.
distance matrix method, simultaneously invented by Mike Steel and James
Lake. This method is particularly adept at reconstructing relationships
among sequences that have evolved by a non-homogenous (in relation to base
composition) process. Also known as LogDet.
evolutionary event where two identical changes occur independently. For
instance when two homologous sequences possess an isoleucine at a particular
position, and both isoleucines are substituted for leucines. The ancestral
state is the same in both instances and the new character state is the
same. The difference between this type of event and a convergence
lies in the identity of the ancestral state.
molecular sequence data, these are characters where one character state
is observed in at least two sequences and a different character state is
observed in at least two others.
PAUP This program is
the most important program for those who wish to reconstruct phylogenetic
relationships. It is a stand-alone program and runs on Apple macintosh™,
Windows™ and UNIX operating systems. It can deal with DNA and protein
sequences as well as morphological data or any binary or multistate character
data. It is maintained by David
Swofford and is available for purchase from Sinauer Associates.
PAUP* see PAUP.
PAUPSTAR see PAUP.
Permutation Tail Probability
PHYLIP The name of
a package of programs for inferring phylogenies. More information
may be found at the PHYLIP webpage:
This is the scientific discipline of resolving the relationshipd among
and between organisms. It is one of the three branches of Systematics.
Phylogram This is
a phylogenetic tree that indicates the relationships between the taxa and
also conveys a sense of time or rate of evolution. The temporal aspect
of a phylogram is missing from a cladogram.
Phylowin A graphical
program for reconstructing phylogenetic relationships. It runs on
almost all UNIX platforms and performs
and Distance analyses, with bootstrap
resampling. See the website at http://pbil.univ-lyon1.fr
Positive Darwinian Selection
This is a phenomenon wherby there is a selective pressure favouring change.
It is usual to think of natural selection as a process of editing genetic
change so that only a small number of mutational events are retained in
a population. With positive selection, the retention of mutations
is much closer to the rate of mutation. Detection of positive darwinian
selection is usually carried out by estimating the rate of synonymous to
non-synonymous substitutions. If they are equal or if non-synonymous
substitutions appear to be occuring more frequently than synonymous substitutions,
then we can surmise that positive selection is acting on the protein sequence.
PTP Permutation Tail Probability
test. This is a matrix randomisation test. The columns of a
matrix are randomised so that the consensus sequence and the composition
for any particular column is maintained, but any signal is lost.
Any measure of a tree (say tree length) should be much worse from the permuted
data than from the original data except when the original data is
no better than random in the first place.
PUZZLE This is a program
for reconstructing phylogenetic relationships using a quartet method.
It is available from:
Choose the first letter of your term.