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Glossary of terms in phylogenetics

Taxonomy

 * A basonym is the original name of a new combination or the original name of a nomen novum.
 * A new combination is a validly published species transferred to another genus, or a validly published subspecies transferred to another species. The author who makes the transfer should indicate the formation of the new combination by the addition to the citation of the abbreviation "comb. nov.".
 * A nomen novum is a new combination for which an author is obliged to substitute a new specific epithet or a new subspecific epithet as a result of homonymy. The author who makes the transfer should indicate the formation of the nomen novum by the addition to the citation of the abbreviation "nom. nov.".
 * Candidatus provisional status Candidatus for incompletely described procaryotes for describing procaryotic entities for which more than a mere sequence is available but for which characteristics required for description according to the Bacteriological Code (1990 Revision) are lacking.
 * sp. abbreviation for species, when following a genus name and followed in turn by a strain name it implies a strain which could not be accurately be classified to a species

Phylogenetics
Accuracy The ability of a method to recover the correct solution. For phylogenetic reconstruction methods, this may be assessed in terms of consistency, efficiency, and robustness.

Additive tree A phylogenetic tree in which the distance between any two points is the sum of the lengths of the branches along the path connecting two points.

Alignment The juxtaposition of amino acids or nucleotides in homologous molecules to maximize similarity or minimize the number of inferred changes among the sequences. Alignment is used to infer positional homology (q.v.) prior to or concurrent with phylogenetic.

Apomorphy A derived character state.

Autapomorphy A derived character state unique to a particular taxon.

Bifurcation A node in a tree that connects exactly three branches. If the tree is directed (rooted), then one of the branches represents an ancestral lineage and the other two branches represent descendent lineages. Synonym: dichotomy.

Bootstrapping A statistical method based on repeated random sampling with replacement from an original sample to provide a collection of new pseudoreplicate samples, from which sampling variance can be estimated.

Character A variable feature that in any given taxon or sequence takes one out of a set of two or more different states (e.g., eye color or amino acid position 12 of a particular protein).

Character state The specific value taken by a character in a specific taxon or sequence (e.g., green eyes or glycine at position 12 of a particular protein). See character.

Cladogram A tree that depicts inferred historical branching relationships among entities. Unless otherwise stated, the depicted branch lengths in a cladogram are arbitrary; only the branching order is significant. See phylogram.

Cluster analysis A rapid method of hierarchically grouping taxa or sequences on the basis of similarity or distance.

Coalescence The evolutionary process viewed backward through time, so that allelic diversity is traced back through mutations to ancestral alleles. Coalescent theory can be used to make predictions about effective population sizes, ages and frequencies of alleles, selection, rates of mutation, or time to common ancestry of a set of alleles.

Congruence Agreement among data or data sets.

Consistency A measure of the ability of a particular method to converge on the correct answer as the sample size becomes infinite.

Dendrogram Any branching tree-like diagram.

Efficiency A measure of how quickly a particular method converges on the correct solution as more data are applied to the problem.

Gene tree A branching diagram that depicts the known or (usually) inferred relationships among an historically related group of genes or other nucleotide or amino acid sequences.

Heuristic method Any analysis procedure that does not guarantee finding the optimal solution to a problem (usually used to obtain a large increase in speed over exact methods).

Homology Common ancestry of two or more genes or gene products.

Homoplasy A collection of phenomena that leads to similarities in character states for reasons other than inheritance from a common ancestor. These include convergence, parallelism, and reversal.

Ingroup An assumed monophyletic group, usually comprising the taxa of primary interest.

Isology Sequence similarity of aligned nucleic acids or polypeptides; the similarity may be due to homology or convergence.

Jackknifing A statistical method of numerical resampling based on deleting a portion of the original observations in subsequent samples (see Chapters 10 and 11).

Maximum likelihood 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 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 1. Originally, a name applied to a phylogenetic optimality criterion developed by A. W. F. Edwards. 2. The name applied by Rzhetsky and Nei (1992) to a phylogenetic optimality criterion that was originally described by Kidd and Sgaramella-Zonta (1971). The optimal tree under this criterion is the tree with the smallest sum of branch lengths as estimated under the least-squares criterion, with negative branch lengths disallowed.

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

Most-parsimonious reconstruction (MPR) Any assignment of ancestral states to characters on a tree so that the change of each character is minimized (subject to any constraints being enforced).

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).

Neighbor joining An heuristic search algorithm for finding a minimum evolution tree.

Nonsynonymous substitution A nucleotide substitution that results in an amino acid replacement.

Objective function (optimality criterion) A function that defines how well data fit a particular hypothesis (as, for instance, a particular phylogenetic tree).

Orthology Homology that arises via speciation.

OTU Operational taxonomic unit. Synonymous with terminal taxon.

Outgroup One or more taxa assumed to be phylogenetically outside the ingroup that are used as a rooting point of a phylogenetic tree and may be used to assign the direction of change to character-state transformations.

Paralogy Homology that arises via gene duplication.

Phenogram A branching diagram that links entities by estimates of overall similarity. Usually constructed using UPGMA cluster analysis.

Phylogeny The historical relationships among lineages of organisms or their parts (e.g., genes).

Phylogeography The study of biogeography as revealed by a comparison of estimated phylogenies of populations or species with their geographic distributions.

Phylogram A tree that depicts inferred historical relationships among entities. Differs from a cladogram in that the branches are drawn proportional to the amount of inferred character change.

Plerology Homology of repeated sequences that are subject to concerted evolution.

Plesiomorphy An ancestral character state.

Repeatability A measure of how often a method converges on the same solution (not necessarily the correct solution) with a given amount of data.

Reticulation Connection between lineages that had previously branched (can be represented graphically by a network)

Robustness A measure of how sensitive a particular method is to violation of its assumptions.

Star treeA tree that contains a single internal node.

Symplesiomorphy A shared ancestral character state.

Synapomorphy A shared derived character state that is indicative of a phylogenetic relationship among two or more OTUs.

Synonymous substitution A nucleotide substitution that does not result in an amino acid replacement.

Transition A nucleotide substitution from one purine to another purine (e.g., A->G), or from one pyramidine to another pyramidine (e.g., T->C).

Transversion A nucleotide substitution from a purine to a pyramidine (e.g., A->C), or vice versa (e.g., T->G).


 * Tree length The sum of the estimated or actual branch lengths in tree.
 * Unrooted tree A phylogenetic tree that is not directed with respect to time.
 * Xenology Homology that arises via lateral gene transfer between unrelated species (e.g., by retroviruses).