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Systematic Biology Primer


At a Glance

Systematics/Systematic Biology: Biological information organized in a taxonomic or phylogenetic manner.

Phylogeny: The natural, evolutionary relationships between groups of living things, inferred using a variety of techniques to establish the relative importance of various shared features (apomorphies and plesiomorphies).

Taxonomy:The science of organizing (= classifying) living things into groups reflecting their natural, phylogenetic relationships. Such groups are called taxa (sing. taxon).

Nomenclature: The assignment of correct names to taxa.


The systematic classification of living, or once living, things – which these days is encouraged to be consistent with their presumed evolutionary relationships (“phylogeny”) – is called taxonomy. Naming them, an exacting pursuit in itself, is called nomenclature. Systematics is where taxonomy and nomenclature meet; biological reviews which organise their material in a taxonomic or phylogenetic manner are referred to as “systematic.”

Phylogeny is the true evolutionary relationships between groups of living things. The adjective is phylogenetic and the study of phylogeny is phylogenetics.

It is intuitively obvious that there exists a hierarchy of phylogenetic relationships among living things. Different kinds of cat are clearly more similar to one another than to any of the various kinds of dog, and vice versa. Moreover, cats and dogs are clearly more similar to each other than either is to a frog, or a fish, or a housefly.

In fact, using intuition alone, we can easily construct a hierarchy of similarities among these groups of animals, such as that shown in fig. 1, with which few would argue. Such an illustration is called a cladogram.

primer graph
Fig. 1: Intuitive relationships between some familiar animals.

Unfortunately, when the broader range of living things is considered, intuition quickly fails us. Is a sea snail more like a crab, or a starfish?* To answer questions like this, organisms must be analysed in great detail, and the similarities carefully evaluated to determine their phylogenetic significance, if any. The process is subjective, and today's “truth” is always provisional.

It might seem that the comparison of gene sequences between taxa can provide an objective measure of similarity. Perhaps, one day, it may be so. For the present, unfortunately, genetic evidence is as open to interpretation as any other.
* The view today is that the most fundamental division within the bilateral animals is between the protostomes and the deuterostomes. Both sea snails (which are types of mollusc) and crabs (which are arthropods) are protostomes, whereas starfish (echinoderms) are deuterostomes. Thus snails are more like crabs than starfish.

The science of organizing living things into groups which reflect their natural, phylogenetic relationships, is called taxonomy. The groups are called taxa (sing. taxon, see below).

The division of familiar objects into animal, vegetable and mineral probably dates back to prehistory, and it is commonplace to hear the phrase “animal kingdom” or “plant kingdom.” Most students will be aware, also, of the landmark contribution made by the Swedish naturalist, Carolus Linnaeus (and variations on that spelling) in the mid-1700s.
Today we still use a derived form of the categories first published by Linnaeus, although much of the detail has changed. For example, many single-celled organisms – none of which were known to Linnaeus – are regarded as belonging to a kingdom of their own, the Protista, which stands alongside the Animalia and Plantae. The fungi are no longer considered plants; they too have a kingdom to themselves.

Most surprising, however, was the discovery arising from genetic studies that protists, plants, animals and fungi, collectively known as the Eucarya, are all relatively similar to one another, compared to the far more fundamental differences dividing them from two great lineages of bacteria, the Archaea and the Bacteria. These three “domains” – the Archaea, Bacteria and Eucarya – are now considered the most fundamental divisions of living things.

From highest (most inclusive) to lowest (most specific), the major formal taxonomic units, or “ranks” are:

  • Domain
           (= Superkingdom)
  • Kingdom
  • Phylum (often called a
           “Division” in botany)
  • Class
  • Order
  • Family
  • Genus
  • Species

Intermediate divisions are often used, “subspecies” and “variety” being very commonly employed at the lower end.

Taxonomic Units (or ranks)

Taxon (pl. Taxa)
The published groups within each of the divisions in the phylogenetic hierarchy is known as a taxon. Like the relationships themselves, taxa fall into a hierarchy.
The lowest level taxon in most cases is the familiar species, which one can informally think of as a group of organisms which are so closely related that they can inter-breed freely. (This concept obviously fails for organisms which reproduce asexually, and in other circumstances also, but it is sufficient for now.

Above the species level, grouping together similar species, is the genus (pl. genera). A familiar example of a genus is Pinus, to which several different but related species of pine tree belong. Above that again is the family, and so on.

To identify an organism is to determine which taxon it belongs to. An “accurate” identification is not only correct, but will identify an organism with a particular species.

However, it is not at all unusual, in practice, that an identification can only be made to genus or even higher level. There are many possible reasons. Perhaps the organism being identified is incomplete; some part (e.g. a flower) which is necessary for a completely accurate identification is not present. This problem is particularly acute when it comes to identifying fossils, which are more commonly fragmentary than not. In some cases, the species may not have been previously recognized, or even if recognized, not formally published.

In such cases, a relationship to a similar species which has been described might be indicated with an aff. indicating “;affinity to,” or the less confident cf. meaning “compare with.”

In order to communicate biological information, it is essential to have universally understood “name tags” for the biological entities we are referring to. This labeling is theoretically possible by means of formulas or letters, though they are not euphonious and would be mnemonically difficult for most people. Instead, Latinized names are employed.

“The purpose of formal nomenclature is to provide a precise, simple, and stable system of unique names used by scientists in all countries. The system must allow for reasonable expansion and refinement to accommodate increasing knowledge. In other words, the stability must not become a straitjacket” (Traverse 1996, p. 13).

Homonyms and Synonyms
Homonyms are identical names for two different taxa.
Synonyms are different names for the same taxon.

Neither can be tolerated in a rational nomenclature. As a general rule, when these situations arise it is the first name to be published which is retained. However, the correct outcome is not always obvious because the distinction between taxa is often quite subjective. In fact, there are colloquial terms in common usage for scientists to tend to create inclusive taxa, with quite broad accommodation for variety (they are called “lumpers”) as opposed to those who subdivide very finely, creating taxa which accommodate very little variation at all (“splitters”). And, in fact, there is no “right” answer: man classifies; nature does not.

As we have seen, phylogeny is the evolutionary relationships among organisms. The patterns of lineage branching produced by the true evolutionary history of the organisms being considered comprise a hierarchy, for which the common metaphor is a tree. We often hear reference to a family tree, or even a branch of a family tree, in our daily lives.

A branch on such a tree is defined by context: we may be referring to a single twig which has no dependent parts, or to quite a large branch which has many smaller branchlets or twigs depending from it. In either case, such a branch is called a “clade.”

“Cladistics” is the word we give to the study of clades, and it is not substantively different from phylogenetics - the study of phylogeny. If there is any useful difference at all, it is a matter of emphasis: whether upon lineages (cladistics) or relationships (phylogenetics).

We have seen above that a clade is a branch on a tree of descent. Anything occurring outside that branch, further towards the root of the tree, is an outgroup.

The distinction is more than simply contextual: For example, in order to calculate the similarity of genome sequences, it is essential to include within the study one or, preferably, several taxa that lie outside the group in which we are trying to detect relationships. If we are interested in determining the relationships of tigers, we would use close relatives of tigers as our outgroups.

Outgroup comparison is the way we determine how widespread a particular feature may be, whether it is found only within the group (apomorphies) of interest, or beyond that group.

Monophyly (Monophyletic Group)
A monophyletic group is one which includes an ancestral species and all its descendants. It is a complete clade.

As we have seen, a monophyletic group can be extremely large and inclusive – for example, most people today would agree the legions of different kinds of insects comprise a monophyletic group – or quite small and exclusive – ex: the enigmatic sea spiders (class Pycnogonida)

Paraphyly (Paraphyletic Group)
A paraphyletic group is a clade lacking some of the descendant species.

Today there is a movement away from applying formal names to groups which are known to be paraphyletic, although some of the old taxa are still very useful even though they are now believed to be paraphyletic.

Perhaps the best example is the reptiles. Because both mammals and birds evolved from reptilian ancestors, but are not included in the class Reptilia, the latter is clearly paraphyletic and a cladistic purist might prefer not to use the name. However, the meaning and scope of the reptile class is still a very well understood and useful concept.

What is more, if we were to blindly enforce “Russian doll nomenclature” in this fashion, it seems unlikely the existing hierarchy of taxonomic ranks will cope.

Polyphyly (Polyphyletic Group)
A polyphyletic taxon is an “unnatural” assemblage of two or more clades, united by some characteristic which is not a primitive feature (plesiomorphy).

Groupings which are thought to be polyphyletic truly are avoided by taxonomists, which is one reason there are not too many familiar real examples. An artificial example is “warm blooded animals,” a group which includes both mammals and birds. However, both these groups arose, at different times, from cold-blooded (reptilian) stock: their warm-bloodedness is not an apomorphy, but it evolved separately, and is different in detail.

Again, however, all is not plain and simple. Some taxa, even those with a long history of study such as the arthropods, are still subject to on-going controversy. Although most researchers are of the view that the Arthropoda are a "good" monophyletic clade, there remain a few who argue that the arthropod characteristics were arrived at separately by more than one lineage, and thus the group is polyphyletic. They are in a small minority, but some small doubt remains.

Nielsen, Claus 2000 Animal Evolution. Second Edition. 563 pp. Oxford University Press.
Traverse, A. 1996: Nomenclature and Taxonomy: Systematics. In Jansonius, J.; McGregor, D.C. (eds.) 1996: Palynology: Principles and Applications. American Association of Stratigraphic Palynologists Foundation, v. 1: 11-28.
Tudge, Colin 2000: The Variety of Life. Oxford.

Pterophyllum Altum - Pellegrin 1903

Peixes do Rio Negro Peixes do Rio Negro/Fishes of the Rio Negro by Alfred Russell Wallace (1850–1852); Mτnica de Toledo-Piza Ragazzo (ed.). 2002

The Naturalist on the River Amazons by Henry Walter Bates

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