Glossary of terms used in Phylogeny Reconstruction.
T
Taxon (pl. taxa)
Also known as an operational taxonomic unit (OTU). This is an individual,
a strain, a species or any unit of classification. In phylogeny reconstruction,
the contemporary or hypothetical ancestral strain, species or whatever,
is known as a taxon. A hypothetical ancestor, a fossil and a clade
are also known as taxa.
Taxonomy This is
the scientific discipline of naming organisms. It was started by
Carolus Linné (Carl Linneaus), perhaps the most famous taxonomist.
Taxonomy is one of the three branches of Systematics.
TBR see Tree-bisection-reconnection.
Transition (Ti)
This is a substitution of a purine
for a purine or a pyrimidine
for a pyrimidine (like-for-like),
Transition-transversion ratio (Ti/Tv)
(1) This is a ratio of the number of transition to transversion substitutions
that appear to have occurred since two sequences separated from a common
ancestor. (2) This is the average rate of transition versus transversion
substitutions in a dataset. (3) This is a value, estimated by reference
to a tree that describes the average rate of transition to transversion
substitutions during the evolutionary period covered by the tree. Note:
Transition-transversion ratio was previously known by the acronym Ts:Tv
ratio. However, since this is a well-known acronym for Transsexual-Tansvestite,
it is thought that Ti/Tv is a more appropriate acronym and removes any
confusion.
Transversion (Tv)
This is a substitution of a purine
for a pyrimidine or vice versa.
Tree-Bisection-Reconnection
(TBR) This is a heuristic
algorithm for searching through treespace. It proceeds by breaking
a phylogenetic tree into two parts and then reconnecting the two subtrees
at all possible branches. If a better tree is found, it is retained
and another round of TBR is initiated. This is quite a rigorous method
of searching treespace. It is not guaranteed to find the optimal
tree, but it is more robust than SPR or
NNI.
Tree length The
total number of steps required in in order to map a dataset onto a phylogenetic
tree. This term is used both for the Maximum
Parsimony criterion and the Minimum Evolution
objective function.
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