Phylogenetic Jargon

== apomorphy ==
A derived character of a group of organisms, not shared with ancestors of a group of organisms. Apomorphies are unique to the group, and are therefore group-defining.
== bootstrap ==
A technical statistical procedure for estimating the variability of a measurement. In phylogenetics, bootstrapping involves the production of a new, pseudo-dataset by randomly pulling data points from the original dataset. For each pseudo-dataset, a new phylogeny is inferred. Rounds of this provide an estimation of the well- and poorly-supported regions of the original phylogeny.
== character ==
An observable feature of an organism useful for distinguishing it from another. For example, a nucleotide in a DNA sequence, an amino acid in a protein sequence, or morphological characters like hair, feathers, or the presence or absence of certain bones.
== cladistics ==
A class of phylogenetic techniques that construct trees (cladograms) by grouping taxa into nested hierarchies according to shared derived characters (synapomorphies). Cladistics is closely associated with the parsimony criterion.
== cladogram ==
A hierarchical classification of taxa represented as a tree. Cladograms formally are independent of evolutionary theory, though in practice they are usually interpreted as phylogenies.
== derived character ==
See apomorphy.
== least squares ==
A phylogenetic distance matrix criterion. The best tree is the one with the smallest squared difference between the observed pairwise distances and the distances calculated from the inferred tree. It has a strong statistical justification, as it is based upon the common linear least squares statistical technique. Least squares is guaranteed by the Gauss-Markov theorem to converge on the correct answer as more data is included in the analysis if a proper distance metric is used, i.e. least squares is statistically consistent. Weighted versions correct for random variability and bias due to longer branch lengths.
== maximum likelihood ==
A cladistic criterion for inferring trees with character conflict. The best tree and evololutionary model maximize the probability of the observed data. Maximum likelihood has a strong statistical foundation. Given a correct model of evolutionary change, it is guaranteed to be statistically consistent, i.e. it will converge on the correct tree as more data is added. Maximum likelihood generally performs the best of all methods in simulations, but it is very computationally expensive. Unlike parsimony, it explicitly relies upon a specific evolutionary model.
== minimum evolution ==
A phylogenetic distance matrix criterion. The best tree is the one in which the sum of the branch lengths is smallest.
== neighbor-joining ==
A distance matrix algorithm for inferring trees. It is an approximation to the least-squares and minimum evolution methods.
== node ==
A point in a phylogeny where branches meet or end. Nodes at the tip or end of a branch represent taxa. In rooted trees, internal nodes represent common ancestors.
== parsimony ==
A phylogenetic criterion for inferring trees with character conflict. Parsimony requires that the best tree is the one with the least character conflict. It is known to produce the incorrect phylogeny in certain cases, such as when evolutionary rates are high or certain branches are long.
== phenetics ==
Sometimes known as numerical taxonomy, phenetic methods classify and group organisms based on overall similarity, usually without explicit reference to their phylogenetic relationships.
== phylogeny ==
A branching, tree-like diagram representing genealogical relationships among taxa. Rooted phylogenies specify common ancestors and have a time axis.
== plesiomorphy ==
A primitive character, shared with the ancestors of a group of organisms. Since it is common to more than just the group being considered, a plesiomorphy is not group-defining.
== primitive character ==
See plesiomorphy.
== root ==
A common ancestor of all taxa in a phylogeny. Chronologically, the root is the oldest node.
== synapomorphy ==
A derived character that is shared between two groups of organisms.
== UPGMA ==
A distance matrix-based clustering method for constructing trees. Rarely used, it is very fast but assumes constant evolutionary rates throughout the tree (a property called ultrametricity).