Glossary of terms used in Phylogeny Reconstruction.



Paralinear distancesA 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.

Parallelism An 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.

Paralog This is a gene from the same homologous superfamily found in another part of the genome of a particulat taxon.  Paralogs are the result of a gene duplication, not a lineage splitting event.

Parsimony-informativeFor 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.



Permutation Tail Probability Test see PTP.

PHYLIP The name of a package of programs for inferring phylogenies.  More information may be found at the PHYLIP webpage:

Phylogenetics 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 Parsimony, Likelihood and Distance analyses, with bootstrap resampling.  See the website at

Polarise The ability to be able to identify, a priori, character states that are ancestral and those that are derived. This is usually not possible with molecular data.

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.

Purine An Adenine or a Guanine nucleotide.

PUZZLE This is a program for reconstructing phylogenetic relationships using a quartet method.  It is available from:   You can view the manual here.

Pyrimidine A Cytosine or a Thymidine nucleotide.

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Any Questions? email: James.O.McInerney