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.
Silent substitutions see
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
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.
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,
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
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
Swofford, Dave The
author of the PAUP/PAUP* computer program for reconstructing phylogenetic
relationships. Contact information is available at www.lms.si.edu.
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
Systematic bias see Systematic error.
Choose the first letter of your term.