Glossary

- taken & adapted from Hillis et al (1996), Majerus et al (1996) and Walker (1989)

Paralogy: Homology that arises via gene duplication.

Paraphyletic: A taxon that excludes species that share a common ancestor with its members.

PCR: see Polymerase chain reaction.

Phenetics: Classification based on overall similarity in as many characters as possible, usually without weighting.

Phenogram: A branching diagram that links entities by estimates of overall similarity.

Phenotype: The observable properties of an organism, resulting from the interaction between the organism's genotype and the environment in which it develops.

Phylogeny: The historical relationships among entities. Differs from a cladogram in that the branches are drawn proportional to the amount of inferred character change.

Phylogenetic tree: A diagrammatic representation of genetic distances between populations, species or higher taxa, the branching of which is said to resemble a tree.

Plesiomorphy: An ancestral character state.

Polymerase chain reaction: A method of amplifying specific DNA sequences by means of repeated rounds of primer-directed DNA synthesis.

Polymorphism: The presence of several forms of a trait, gene or DNA sequence in a population.

Polyphyletic: A group of taxa that are derived from two or more ancestral forms not common to all members, (opposite of monophyletic).

Pseudogene: A gene showing significant sequence homoplasy (>75%) to a functional gene, but which has lost any normal function, often through gaining internal stop codons.

Random genetic drift: Fluctuation in the frequencies of neutral genes and neutral alleles in a population due to the fact that each generation is only a sample of the one it replaces.

Ribonucleic acid: A polynucleotide consisting of a chain of sugar and phosphate units to which are attached various nitrogenous bases, (adenine, cytosine, guanine and uracil).

Sexual selection: Selection which promotes traits that will increase an organism's success in mating and ensuring that its gametes are successful in fertilisation. This is distinct from natural selection which acts simply on traits which influence fecundity and survival.

Species: A cohesive historical lineage of ancestral-descendant populations of organisms that maintains its identity from other such lineages. A species comes into being at a branching event (when one lineage becomes one or more lineages), and ceases to exist either at a branching event (when it gives rise to new species) or when the lineage is terminated through extinction.

Symplesiomorphy: A shared ancestral character state.

Synapomorphy: A shared derived character state that is indicative of a phylogenetic relationship among two or more OUT's.

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).