The three components of systematics can be described as follows:
Taxonomy
Taxonomy is a process. In this process, a classification (see below) can be referred to but its
focus is on the study and description of the objects being classified. It includes the examination
of individual organisms and the description, analysis and quantification of taxa by way of the
characters they possess. Characters can be taken from morphology (gross morphology to cellular
ultrastructure) and at different life history stages (cell division cycles to adults with
indeterminate growth). Molecular characters underlie this morphology and scale from base pair
to genome. Because of this complexity, character analysis of semaphoronts is critical for the
accurate scoring of character states whether it is the homology of morphological structures or the
alignment of gene fragments.
The practice of taxonomy requires an extraordinary understanding of a taxon and the ability to
rigorously extract and evaluate the necessary character information. To do this systematists may
require access to microscopy, imaging, histological and molecular facilities, or some subset of
them. For extinct taxa, access to isotopic, thin-section and 3D reconstruction technologies may
also be necessary. Unfortunately, and often not from necessity, the taxonomy of many groups is
based on little more than a handful of traditional characters.
Taxonomy interacts with both nomenclature and classification (Fig. 1). The taxonomic study
describes the characters, and their states, of a taxon or taxa. Through interaction with
nomenclature a name can be attached to specimens (grouped as taxa) with unique sets of
character states.
The interaction of taxonomy with classification requires an additional step – an analysis of the
character states, preferably an algorithmic one. There are three major kinds of analysis:
evolutionary systematics, phenetic and cladistic. In evolutionary systematics the analysis is
largely dependent on the systematist’s intimate knowledge of the group to produce an
evolutionary scenario. Similarly, cladistic techniques can be applied without using computers but
modern phenetic and cladistic analysis use numerical algorithms and are more computational.
Phenetics uses clustering techniques based on overall similarity of the data (e.g., UPGMA and
neighbor joining) while cladistic and other phylogenetic reconstruction methods use special
similarity (e.g., parsimony) or require an evolutionary model and parameters (e.g., maximum
likelihood or Bayesian analysis). Regardless of the method of analysis of the taxonomic data, the
process produces a classification.
Classification
Like the term taxonomy, classification is commonly used outside the biological systematic
community as almost any animate or inanimate object, place, concept or event can be classified
according to some criteria or scheme. It is the act of assigning individuals to a class or classes
based on some common relations or affinities. Biological classifications, produced by phenetic
and cladistic computations, are trees of hieratical relationships. In evolutionary systematics
classifications may be represented by assignment of ‘taxonomic’ rank (species, genera, families,
superfamilies, orders etc.) or by evolutionary scenarios. Classifications may or may not reflect
putative evolutionary relationships (phylogenies) and when characters are heavily weighted or
the groupings are based on algorithms that feature overall similarity, there is a far greater
probably that the classifications will not reflect evolutionary history.
Classification interacts with both taxonomy and nomenclature (Fig. 1). With classifications that
provide trees, the tips and nodes can be formally named following nomenclatural practices.
Classifications provide predictions that can be tested by examining additional taxa or characters.
Previously unstudied taxa can be predicted to have certain character states while the discovery of
homoplasy may necessitate reexamination of the study taxa to document putative convergences.
Classification also provides an important interface to other biological enterprises. The benefits of
using classifications that reflect the evolutionary history (phylogeny) of a taxon in research,
conservation and economic ventures is being increasingly recognized throughout the biological
sciences. Unfortunately, the replacement of existing classifications by new classifications that
reflect phylogeny often require name changes at various taxon levels that can cause short term
angst, but the classification is not the problem. Name changes are nomenclatural (see below).
The tips of the trees in classifications may be an individual, a composite taxon (population,
species, genus, etc.), or a grade. They do not necessarily have or need formal names and a tree of
microcentrifuge tube numbers may be all that is necessary to test competing hypotheses.
Nomenclature
Nomenclature in biological systematics is the assigning of formal names to all or some of the tips
and nodes of a hierarchical classification. The International Code of Zoological Nomenclature
(ICZN) provides rules on how taxa will be named and how conflicts in nomenclature (not
classification) will be resolved. Recently, alternative systems of nomenclature have been
proposed [BioCode and Phylocode (http://www.ohiou.edu/phylocode/)], but neither have yet
gained general acceptance.
Nomenclature interacts with classification by providing names (and typically ranks1) for the
different groupings present in the classification and with taxonomy by providing unique names
to distinct taxa with certain combinations of character states as discussed above. This latter
interaction is well illustrated by the common association of character states and nomenclature in
classic dichotomous keys.
Nomenclature provides a relatively stable name governed by a set of rules (unlike the adoption
of so called “common names”) which allows non-specialists (e.g., conservation and economic
communities) and specialists to communicate. Stable or trackable nomenclature is critical to both
communities. For example, listing of species for environmental protection requires a ‘scientific
name’ and the units used to estimate biodiversity are almost always formal scientific names
1 Under ICZN rules ranks do not need to be assigned for taxa above the family-group. Under Phylocode, ranks are
not assigned except at the species level.
parsed by rank (e.g., species, generic, familial diversity). Names of invasive species must be
globally understood to be effective in restricting movement. Likewise for the recognition of
parasite vectors and patents for natural compounds and the regulation of commercial and sport
fisheries.
