Teaching Animal Molecular Phylogenetics

Glossary

GLOSSARY (click the BACK button on your browser to return)
See also the "Glossary of terms used in Phylogeny Reconstruction" at www.may.ie/academic/biology/james/Glossary.html

18S rDNA. DNA sequence that encodes 18S ribosomal RNA, which is the RNA in the smaller subunit of metazoan ribosomes. Also called SSU rDNA (small subunit ribosomal DNA). 18S indicates the sedimentation factor of the RNA.

Alignment. Adjustment of the position of two or more molecular sequences relative to each other so that homologous positions of the molecule can be compared.

Apomorphic. Derived, as opposed to primitive (plesiomorphic).

Bootstrapping. A technique for estimating the reliability of an internal branch of a tree by resampling the original data set. With DNA sequences the bases at each position are randomly sampled then returned to the pool so that they may be resampled again. The bootstrap value for a branch is the percentage of such resamplings (typically 500 to 1000) that recover the branch. Compare Jackknifing in which resampling is done without replacement, and Parametric bootstrapping in which the sequences to be resampled are generated by numerical simulation.

Collapsing. Eliminating a poorly supported branch by merging the nodes at each end of it.

Consensus tree. A tree that is supported by two or more methods, possibly as the result of collapsing internal branches that are not supported by all methods.

DNA-DNA hybridization. A technique, now seldom used, that determines the degree of similarity between DNA sequences from two taxa by separating the DNA into single strands, allowing them to hybridize into a double strand, and measuring the temperature at which the strands separate again.

EF-1∝. Elongation factor-1∝. One of several proteins involved in the synthesis of proteins by ribosomes in eukaryotes. It helps bind aminoacyl-tRNAs to ribosomes during translation.

Elongation factor. A protein involved in translation. See EF-1∀.

Exhaustive search. A search for the optimal tree among all possible ones. Compare Heuristic search.

Heuristic search. A method of reducing the number of trees to be searched when the number is too large for an exhaustive search.

Homeotic. Referring to a gene that directs the appropriate development of a body segment.

Homoplasy. The occurrence of similar characters in two taxa by convergent evolution rather than by inheritance from a shared ancestor. Analogy.

Hox genes. Developmental regulatory genes that occur in clusters. They are best characterized in segmented animals, where they control the identity of each segment depending on anterior-posterior position.

Informative site. A molecular site with two or more character states, at least two of which occur in two or more taxa each.

Jackknifing. A technique for estimating the confidence in an internal branch of a tree by resampling the original data set without replacement, so that no datum is used more than once. With DNA sequences a certain percentage of the positions are sampled and a new tree is reconstructed. The jackknife value for the branch is the percentage of such resamplings (typically 500 to 1000) that recover the branch. Compare Bootstrapping, in which resampled data may be used more than once.

Log likelihood (ln L). A measure of the likelihood of a tree as inferred from the maximum likelihood method.

Long-branch attraction. The tendency of taxa that have evolved rapidly or for long times to appear to be more closely related than they are.

Long interspersed element (LINE). DNA sequence of 3 to 7 kb (kilo-base pairs) that has no known function except producing enzymes that reverse-transcribe other copies of themselves from RNA and introduce the copies into the genome. See also Short interspersed element (SINE).

Maximum likelihood (ML). An approach to tree construction that begins with the possible trees and deduces which one is most likely given the data and an explicit model of evolution.

Maximum parsimony (MP). A cladistic approach to tree construction that tries to find the tree with the fewest changes among informative sites.

Neighbor-joining (NJ). A method of phylogenetic analysis that constructs a tree with the shortest total branch length.

Operational taxonomic unit (OTU). A group tentatively assumed to be a valid taxon for purposes of phylogenetic analysis.

Orthologous. Homologous as the result of speciation but not gene duplication. Orthologous genes are derived from the same copy of a gene in the most recent common ancestor. Compare Paralogous.

Paralogous. Homologous as the result of gene duplication. Paralogous genes are derived from different copies of a gene in the most recent common ancestor. Compare Orthologous.

Parametric bootstrapping. A technique for estimating the reliability of an internal branch of a tree by resampling sequences that are generated by numerical simulation based on a model of evolution. Compare (non-parametric) Bootstrapping.

Paraphyletic. Referring to a group that does not include all the branches from the ancestral node.

Parsimony. The criterion for selecting a tree because it requires the fewest hypotheses about the evolution of a character.

Plesiomorphic. Primitive, as opposed to derived (apomorphic).

Polymorphism. The occurrence of two or more states of a character in a single species.

Polyphyletic. Referring to an artificial group comprising branches from two or more nodes.

Rooting. Determining the origin of a tree, usually by using an outgroup or by fixing it at the midpoint of the longest path between two taxa.

Scaling. Making the length of a branch in a phylogenetic tree proportional to the degree of evolutionary change.

Short interspersed element (SINE). DNA sequence of 75 to 500 bp (base pairs) with no known function that is reverse-transcribed, usually from tRNA, and inserted into the genome with the aid of long interspersed elements (LINEs).

Study group. The group of organisms whose phylogeny is being studied.

Symplesiomorphy. Referring to a character that occurs in the outgroup and is therefore assumed to be plesiomorphic (primitive) in the ingroup.

Synapomorphy. A homologous derived character shared by two or more, but not all, taxa in the ingroup.

Total-evidence tree. A tree constructed by using both morphological and molecular evidence.

Transition. Change from one purine to another (adenine to guanine or vice versa) or one pyrimidine to another (thymine to cytosine or vice versa). Compare transversion.

Transposable element. Segments of chromosomes that move to different loci.

Transversion. Change from a purine to a pyrimidine (adenine to thymine, for example) or from a pyrimidine to a purine. Compare transition.

Weighting. Giving more value to some character-state changes than to others, generally because they are less common.