Glossary in Phylogeny Construction

M


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.

Maximum Likelihood (ML)

A criterion for estimating a parameter from observed data under an explicit model. In phylogenetic analysis, the optimal tree under the maximum likelihood criterion is the tree that is the most likely to have occurred given the observed data and the assumed model of evolution.

Maximum Parsimony (MP)

A criterion for estimating a parameter from observed data based on the principle of minimizing the number of events needed to explain the data. In phylogenetic analysis, the optimal tree under the maximum parsimony criterion is the tree that requires the fewest number of character-state changes (which may be differentially weighted across characters and/or character-states). Often simply called parsimony.

Minimum Evolution (ME)

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

Monophyletic

A group of taxa that contains an ancestor and all of its descendants.

Multifurcation (Polytomy)

A node in a tree that connects more than three branches. If the tree is directed (rooted), then one of the branches represents an ancestral lineage and the remaining branches represent descendent lineages. A multifurcation may represent a lack of resolution because of too few data available for inferring the phylogeny (in which case it is said to be a soft multifurcation) or it may represent the hypothesized simultaneous splitting of several lineages (in which case it is said to be a hard multifurcation).

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