Apomorphy
The polarity of state of a character that is evolutionarily novel (ie a state shared by descendant members of monophyletic taxa, but not the ancestral species.) For example, tetrapody (four-legged condition) is an evolutionarily novel characteristic shared by amphibians, reptiles, mammals, and birds, but not shared by their ancestral species -- a fish.In a phylogenetic data matrix, apomorphies are coded as "1."
Characters
Characters are attributes or characteristics of species that vary in form or quality. Variations of characters are termed "states." For example, "eye color" might be a character that varies among different species with "red" and "blue" being different states.In a phylogenetic data matrix, characters are represented in columns.
Diversity
Diversity operates at two hierarchical levels. Diversity can refer to numbers of species in a taxon (or geographic area). For example, a wheat-field has little diversity -- it is dominated by a singles species.More often, diversity refers not simple to the number of species, but to the variability and distribution of states of characters) within a group (like a species or monophyletic taxon). Diversity is the result of mutation and meiosis. For example, among sparrows there is little diversity with respect to size: sparrows are all fairly small. Among whales, however, there is more diversity ranging from relatively small pilot whales to the blue whale.
Extinction
Homology
Homology is the assumption that different species can share an apomorphy as the result of common ancestry (phylogeny). For example, it is assumed that humans and birds and snakes and frogs and fish all have vertebrae as the the result of common ancestry rather than that they independently evolved 5 or more times.Macroevolution
Macroevolution represents the overall effects of speciation, extinction, and microevolution and result in patterns of phylogeny within monophyletic taxa. In phylogenetic trees, macroevolution produces branching patterns. Some species have given rise to thousands of other species (e.g. Insects). Most of the species that have ever existed are now extinct. Some species have existed for long periods of time with seemingly little change (like horseshoe crabs).Microevolution
Microevolution represents the overall effects of natural selection and genetic drift on a species. In phylogenetic trees, microevolution results in the slope of lines of ancestor/descendant relationships (phylogeny). For example, when pollution caused tree bark to become darker in Britain, the frequency of dark colored individuals in a population of moths increased (because the others were being eaten).
Monophyletic Taxa
A monophyletic taxon is an ancestral species and all of its descendant species. Monophyletic taxa are the only taxa that are phylogenetically meaningful. The taxonomic group "Birds", for example, is believed to be a monophyletic taxon: all of the birds that we know today are descended from a single species.Phylogeny
Phylogeny is the branching patterns of relationships among species within a monophyletic taxon that result from processes of macroevolution. Inferences about phylogenetic patterns are made based on homology For example, a phylogenetic tree illustrates branching patterns that can be used to explain the distribution of apomorphies and plesiomorphies among a group of taxa.Plesiomorphy
The state of a character that is evolutionarily ancestral (ie, the states of the characters of the ancestral species). For example, tetrapody (four-legged condition) is an apomorphy of the reptiles, but a plesiomorphy of snakes (who have apomorphically lost their legs).In a phylogenetic data matrix, plesiomorphies are represented as "0".
Polarity
States of characters show polarity that can be either plesiomorphic (evolutionary ancestral) or apomorphic (evolutionarily novel). Polarity is always in reference to what is plesiomorphic to a particular monophyletic taxon For example, the lack of flight is the plesiomorphic state for birds, but flight is plesiomorphic to the groups of flightless birds that all had ancestors capable of flight.Species
A species is a group of organisms (or demes) that maintain a common gene pool through interbreeding. Whether or not any two populations of organisms represent a single species is a complex question. Exactly what constitutes a species depends on the context in which the question is asked. For our purposes, if members of populations can not, or do not, interbreed then the populations represent different species.In a phylogenetic data matrix, species are represented in rows.
Speciation
Speciation is the process by which a species gives rise to descendant species, often through mechanisms of reproductive isolation. Increasing numbers of species tends to imply increasing diversity. For example, a population of birds isolated on an island, over time become genetically different from their relatives on the mainland to the extent that they can no longer reproduce even when brought together. At that time, they have become separate species.States
States of characters are forms or variations of particular characters. For example, among different species of beetles, there may be different numbers of tarsal claws: some species may have a state of 2 while others have a state of 3 for the character "number of tarsal claws".In a phylogenetic data matrix, states are represented by 1's and 0's at the intersection of a row (species) and column (character).