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Taxonomy – A Primer


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Introduction

The systematic classification of living, or once living, things – which these days is done to be consistent with their presumed evolutionary relationships ("phylogeny") – is called taxonomy.

It is obvious that there exists a hierarchy of phylogenetic relationships among living things. Our very bodies exemplify such a hierarchy.

 
 

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It is obvious that there exists a hierarchy of phylogenetic relationships among living things. Our human bodies record a sequence billions of years longer than human culture. Nested like painted Russian dolls are features that we share with more and more organisms the deeper we probe. As humans, we have uniquely large brains and upright posture; as primates, fingernails and stereoscopic vision; as mammals, warm blood and milk-fed young; as amniotes (the group that includes mammals, birds, and reptiles) internal fertilization and the ability to reproduce ourselves outside a watery environment. All animals have tissues, and all of us collect our carbon and energy from organic compounds derived from all those plants, algae, and bacteria that can use either chemical energy or light to manufacture their own supplies out of nonliving raw materials. Like almost all organisms except bacteria, we have cells with nuclei and chromosomes, organelles, and an oxygen drive. In common with every living thing we have DNA, genetic blueprints, and metabolism – the equipment to absorb, dismantle, and exploit useful molecules.

The division of life into plants and animals is a rough human classification that works well enough to describe various shapes and expected behaviors but has little to do with how life arose, or how early organisms made a living. Likewise, among living organisms, especially the small ones, the labels “plant” and “animal” represent two collections of features drawn from a much larger total range, and often found in combinations that ignore these simple categories. There are far more lifestyles than these two labels allow for, and some of them are practiced by organisms that live off what we would consider to be inorganic foods. Working from definitions based on fundamental cellular machinery, we now recognize three basic types of living things.

First are the archaebacteria, “ancient bacteria.” Not many species now survive. They evolved on an alien Earth, and now live in extreme environments: hot springs where temperatures never fall below 55 C; salt flats where salinities are four times ocean levels; the intestines of cattle or our own, for that matter.

Second are the “eubacteria,” many thousands of species with an enormously broad variety of lifestyles fermenters, nitrogenfixers, sulfur users, oxygen producers, recycling specialists for all kinds of vital molecules.

Both archaebacteria and eubacteria are prokaryotes, “preseeds,” so called because of the way they carry their DNA loose inside their outer cell membrane. The third fundamental division of life is the “true seeds” (eukaryotes, EKs for short), which package their genes in a “seed” or nucleus, a separate envelope inside the outer membrane. They comprise all of what we consider to be “higher organisms,” including ourselves.

There is one other problematic group, the viruses, which are particularly hard to define. They do not have cells, and probably stem from bits of DNA or RNA that somehow escaped from one or another of the three basic groups. Viruses certainly do not grow, and they feed only if we greatly expand our definition of feeding. In fact, they exist only because they can replicate, and the materials they use in order to replicate are what causes problems; these refugee bits of genetic material’ when bound with proteins, can replicate themselves only by reinvading and subverting living cells.

What do we mean by “sytematics?” First let’s start with a handful of definitions.

Classification – Associating organisms together into various groupings which reflect, as best we know, the relationships between them. There is a hierarchy of such groups, in which the most general group for living things is called a “kingdom” and the most specific grouping called, of course, a “species.” Actually, there can be several finer, less formal, groupings within a species – subspecies, variety, and so on – but for our present purposes it is sufficient to recognise only the following hierarchical divisions:

 

Most general; least specific Kingdom Animalia Linnaeus 1753 There are five or so kingdoms, namely animal, plant, fungi, Protista (= Protoctista), and procaryotes.
  Phylum Chordata The animal phylum Chordata includes all vertebrates. Two other examples are Arthropoda (spiders, insects, crustaceans, etc.) and Pteridophyta (ferns & related plants).
  Subphylum Vertebrata Sometimes the standard hierarchy doesn't offer enough "ranks" to be as useful as it could. In such situations, various intermediate ranks are created below one of the main ranks (sub-) or above one (super-). They are not employed consistently for all groups of organisms. The Vertebrata are animals with backbones.
  Class Mammalia

The class Mammalia includes mammals - warm-blooded, usually furry, vertebrate animals.

As another example of a class, spiders (class Arachnida) are a subdivision of the Arthropoda.

  Order Carnivora The Carnivora includes cats, dogs, bears, including pandas, ferrets, etc. Most carnivores are land animals, but one important group has taken up life in the oceans and includes seals, sea lions, and walruses. (Some authorities regard the seals etc. as comprising an order in its own right.)
  Family Felidae This is, quite literally, the "cat family" which includes nearly forty species of cats, lions, tigers, leopards, cheetahs, etc.
  Genus Panthera There are half a dozen genera of cats. The generally larger members - including the lion, tiger, jaguar and leopard - belong to the genus Panthera. The genus Felis includes a number of wild cats and the domestic moggy. The cheetah belongs to the genus Acinonyx, which differs from most other cats in various respects, such as not being able to fully retract its claws.
Least general; most specific Species leo The lion, Panthera leo.

This hierarchy has evolved from a scheme first developed by the Swedish naturalist, Caroli Linneus, and published by him in his great work, Systema Naturae (1753). (<href="TaxExa.html">More examples.)

Taxon (plural: taxa) – The published groups within each of the divisions in the Linnean hierarchy is known as a taxon. Thus, Animalia, Chordata, Vertebrata, Carnivora, etc. are each taxa, as is the great Siberian Tiger, Felis tigris, figuratively lying in the shade, at the bottom of the tree.
Identification – 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 practise, 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 recognised, or even if recognised, not described. 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.”
Charles Lyell said as early as 1833 of "the genera and orders in zoology and botany [that] we ought to regard them as invented for the convenience of systematic arrangement, always expecting to discover intermediate graduations between the boundary lines that we have first drawn" (quoted in McGowran 1986, p. 35).
Taxonomy ...
Nomenclature ...
“While nomenclature is best kept separate from classification (taxonomy), naming clearly implies differentiation and circumscription. The whole operation of nomenclature and taxonomy together is referred to as systematics” (Traverse 1996, p. 13).

Linnaeus

No discussion of taxonomy could be complete without reference to the giant of modern systematics, Carolus Linnaeus (1707–1778). Linnaeus was a Swede, noted for his arctic expeditions, whose monumental classifications of plants and animals in two major treatises form the basis of taxonomy today.

Both these works, Species Plantarum and Systema Naturae, went through many editions, but the first edition of Species Plantarum (1753) and the tenth edition of Systema Naturae (1758) were eventually adopted in the nineteenth century as the starting points of modern botanical and zoological nomenclature, respectively.
The success of Linnaeus did not simply derive from the sheer number of species he dealt with, nor from his work being the last to provide a single-author comprehensive survey of nature, but primarily from his straightforward use of a clear and uniform hierarchical arrangement of species and groups and his systematic adoption of binomial nomenclature. “Linnaeus, in the eighteenth century, made a great contribution to science by separating classification and nomenclature. Up to that time, scientific names of plants were (increasingly) long descriptive phrases. Linnaeus supplemented these with binary names that eventually replaced the phrases – just two words, a generic name and a specific epithet as modifier. The binomial combination was unique to a particular species: no homonyms or synonyms allowed” (Traverse 1996, p. 13).

Establishment of the Modern Codes

“Following Linnaeus, in the 19th century, the principles he had established began to be gathered into lists of rules to be followed. The lists often conflicted somewhat in fine points, between systematists of various countries. The eventual adoption of universally accepted 'International Codes' occurred in the first decade of [the twentieth] century” (Traverse 1996, p. 13).

References

McGowran, Brian 1986: Beyond Classical Biostratigraphy. PESA Journal, pp.28-41, September 1986.

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.


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