Glossary of terms used in Phylogeny Reconstruction.


SCU Synonymous Codon Usage.  This term refers to the amount of times one codon is used relative to its synonymous alternative(s).  In the late 1960s, it was thought that synonymously-variable nucleotide positions might be neutral with respect to natural selection.  However, it is now known that synonymous alternatives are not used with equal frequency in all genes in all organisms.

Shared-ancestral see Symplesiomorphy.

Shared-derived see Synapomorphy.

Silent substitutions see Synonymous substitutions

Skewness This is a reference to the shape of a histogram of tree lengths that can be produced after searching through treespace.  Studies of random datasets have shown that the distribution of tree lengths is approximately normal, whereas in general datasets with a reasonable amount of signal have few shortest trees and few trees nearly as short.  There is a G-statistic for the skewness of a histrogram.

SPR see Subtree Pruning Regrafting.

Star Decomposition This is a successive clustering method and is a term used to cover a multitude of different algorithms.  Basically, the algorithm proceeds by assuming a 'star' topology

Star Topology This is also known as a bush.  Effectively there is no successive splitting of lineages, rather, all lineages split at the same time, resulting in a topology with a single origin where all external branches radiate from the centre.

Steel, Mike A New Zealand Mathematician, responsible in large part for the development of the LogDet distance matrix method.

Strict consensus tree This a consensus tree formed from more than one fundamental tree.  It only shows those clades that are in complete agreement in all of the fundamental trees.  Also known as a strict component consensus tree.

Subtree Pruning Regrafting (SPR) This is a heuristic search algorithm for searching through treespace.  It proceeds by breaking off part of the tree and attaching it to another part of the tree.  If it finds a better tree, then the new tree is used as a starting tree for another round of SPR.  This is a more rigorous algorithm than NNI, but not as robust as TBR.  Another name for SPR is cut-and-paste.

Successive Approximation Alternatively known as Successive Approximation Character Weighting (SACW).  This is a method of reweighting characters based on some measure of their relative values for the purposes of phylogeny reconstruction.  If, for instance, an initial analysis is carried out and the result of this analysis indicates that some characters are quite inconsistent with the resulting tree(s), then these will be down-weighted in subsequent analyses.  The index for downweighting the characters might be the retention index, consistency index or some such measure of consistency of a character with a tree.  Iterative analyses are carried out, with the individual characters being reweighted each time until there is little or no change in the resulting topology.

Superimposed substitutions Also known as multiple hits.  These are substitutions that have occurred in one or more lineages subsequent to splitting.  However, they are not seen in the contemporary taxa due to having been overlain by more recent changes.

Support Index see Decay Index.

Swofford, Dave The author of the PAUP/PAUP* computer program for reconstructing phylogenetic relationships.  Contact information is available at

SymplesiomorphyThese are characters that are shared by a number of sequences due to retention of the ancestral character state.

Synapomorphy These are characters that are shared by a group of sequences due to recentness of common ancestry.

Synonymous substitutionsThose substitutions that do not change the identity of the encoded amino acid.

Systematics This is an umbrella term to describe the processes that describe species.  There are three disciplines which are united under this broad locution.  First there is the description of species (identification), then there is the naming of names (taxonomy) and then there is the description of the relationships among and between taxa (phylogenetics).

Systematic bias see Systematic error.

Systematic errorThis is a facet of a dataset that will confound any tree reconstruction method.  Situations such as long branch attraction and base-compositional bias are examples of systematic bias.

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Any Questions? email: James Mcinerney