Glossary of terms used in Phylogeny Reconstruction.


MacClade This is a graphical program available exclusively for the Apple macintosh.  It is developed by the Maddison brothers, Wayne and David and is capable of managing data and trees.  It is possible to interactively move the branches of a tree and see how this affects the goodness-of-fit of data to trees.  It is also an excellent accompanying program for PAUP, since trees may be specified, either as constraint trees or fully specified trees and these can be used by PAUP for a variety of tests and searches.

Maddison brothers The Maddison brothers, Wayne and David are the authors of the MacClade program and the Tree of Life project.

Maximum Likelihood (ML) This is a method of inferring phylogenetic relationships using a pre-specified (often user-specified) model of sequence evolution.  Given a tree (a particular topology, with branch lengths), the ML process asks the question "What is the likelihood that this tree would have given rise to the observed datamatrix, given the pre-specified model of sequence evolution?"

Maximum Parsimony (MP) The principle of simpler solutions being preferred over more complex ones.  In relation to phylogeny reconstruction this means that phylogenetic trees that can explain a datamatrix by fewer evolutionary events is preferable over a tree that requires more evolutionary events.

Minimum Evolution (ME) This is an objective function for optimising a phylogenetic tree based on a distance matrix.  ME seeks to find the tree wiith the shortest overall branch lengths.

MOLPHY This is a package of programs specifically designed to facilitate the analysis of DNA and protein sequence data.

Monophyly The making of a monophyletic group.

Monophyletic group A group of organisms with the same taxonomic title (say, genus, family, phylum etc.) that are shown phylogenetically to share a common ancestor that is exclusive to these organisms.

Most Parsimonious Reconstruction (MPR) This is the branching order that requires the fewest number of mutational events in order to explain the comtemporary sequences, for a single character only. This might not necessarily be the same as the most parsimonious tree, as MPR only refers to a single character.

Most Parsimonious Tree (MPT) This is the branching order that requires the fewest number of evolutionary events, when summed over the entirety of the sequences.

Multiple Alignment A multiple sequence alignment is a matrix of data, in which the individual columns represent homologous characters.

Mutational bias The tendency of a region of DNA to become biased in its nucleotide composition. Bias is usually toward high guanine plus cytosine or towards high thymine plus adenine. The effects of mutational bias are more easily seen at nucleotide positions where the selective pressures are not so strong (codon positions where there is a synonymous alternative, intergenic regions, introns etc.).

Choose the first letter of your term.

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

Any Questions? email: James Mcinerney