Glossary of terms used in Phylogeny Reconstruction.




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.

Choose the first letter of your term.

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Any Questions? email: James Mcinerney