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Taxonomy


Abstract

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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.

"Naturalists have striven perpetually to build a meaningful classification scheme for living things. Long before Darwin, plants and animals were believed to be the primary divisions of life. In 1866, Haeckel was the first to challenge this dichotomy by suggesting that the Protista should be considered to be a third kingdom equal in stature to the Plantae and Animalia. The Bacteria or Monera were designated as a fourth kingdom by Copeland, in 1938. Whittaker added the fungi in 1959, and his five kingdom (Plantae, Animalia, Protista, Fungi and Monera) universal tree is still taught as part of basic biology curricula.

 
 

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"Over 50 years ago, Chatton, and Stanier and van Niel suggested that life could be subdivided into two even more fundamental cellular categories, prokaryotes and eukaryotes. The distinction between the two groups was subsequently refined as studies of cellular biology and genetics progressed such that prokaryotes became universally distinguishable from eukaryotes on the basis of missing internal membranes (such as the nuclear membrane and endoplasmic recticulum), nuclear division by fission rather than mitosis and the presence of a cell wall. The definition of eukaryotes was broadened to include Margulis’ endosymbiont hypothesis, which describes how eukaryotes improved their metabolic capacity by engulfing certain prokaryotes and converting them into intracellular organelles, principally mitochondria and chloroplasts.
"In the late 1970s the fundamental belief in the prokaryote–eukaryote dichotomy was shattered by the work of Carl Woese and George Fox. By digesting in vivo labelled 16S rRNA using T1 ribonuclease then accumulating and comparing catalogues of the resultant oligonucleotide ‘words’, Woese and Fox were able to derive dendrograms showing the relationships between different bacterial species. Analyses involving some unusual methanogenic ‘bacteria’ revealed surprising and unique species clusterings among prokaryotes. So deep was the split in the prokaryotes that Woese and Fox proposed in 1977 to call the methanogens and their relatives ‘archaebacteria’, a name which reflected their distinctness from the true bacteria or ‘eubacteria’ as well as contemporary preconceptions that these organisms might have thrived in the environmental conditions of a younger Earth.
"In 1990, Woese, Kandler and Wheelis formally proposed the replacement of the bipartite view of life with a new tripartite scheme based on three urkingdoms or domains; the Bacteria (formerly eubacteria), Archaea (formerly archaebacteria) and Eukarya (formerly eukaryotes although this term is still more often used)" (Brown 2002).
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 fertilisation 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 non-living raw materials. <<< use my own example
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. <<< reword

Taxonomic Ranks

The Variety of Life

For most of us, our perceptions of the living world are mostly shaped by everyday familiarity. We can distinguish and name several kinds of dogs or fruit trees, but probably not so many weevils or wildflowers. Our own large size inclines us to notice and recognise other large vertebrates. We are more likely to be familiar with elephants (or polar bears or kangaroos) which come to our zoos from half a world away, than with the insects in our own gardens. Anything too small to see is a 'microbe' - few of us can distinguish among them; few have much interest. Yet the diversity among 'microbes' far exceeds that of all larger organisms. The most fundamental division of living things is into three categories called superkingdoms; two are exclusively microbial, the familiar plant and animal kingdoms comprise only a small part of the third (fig. 1).

The division of life into plants and animals is a rough human classification that works well enough to describe various shapes and expected behaviours 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.

"Comparison of base or amino acid sequences in non-conserved portions of nucleic acids and proteins, especially the small subunit RNA molecule of the ribosome, have shown that life can be divided into three principal domains: the archaebacteria, eubacteria, and eukaryotes (Woese 1987; Woese et al. 1990; Text-Fig. 1). Some trees indicate a specific sister-group relationship between eukaryotes and archaebacteria (e.g. Gogarten et al. 1989; Iwabe et al.1989; Rivera & Lake 1992). Regardless of the true branching topology of the primary domains, there can be little doubt that these three groups diverged from one another during the Archean Eon" (Knoll 1996).

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.

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 “superkingdom” 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:

rRNA cladogram (8205 bytes)

Fig 1. A rRNA (16S) cladogram showing presumed phylogenetic realtionships between the three superkingdoms: Bacteria (yellow), Archaea (archaeans, green) and Eucarya (eukaryotes, blue). (After Schopf 1999, fig. 4.2.)

Most general; least specific Superkingdom There are three superkingdoms: Bacteria, Archaea and Eucarya.
  Kingdom There are five or so kingdoms, namely animal, plant, fungi, Protoctista, and procaryotes.
  Phylum The animal phylum Chordata includes all vertebrates. Two other examples are Arthropoda (insects, crustaceans, etc.) and Pteridophyta (ferns & related plants).
  Class Vertebrata (a class within the Chordata) are animals with backbones. The trilobites (class Trilobita) are a subdivision of the Arthropoda.
  Order The Carnivora includes cats, dogs, bears, etc., and is a subdivision of the Vertebrata. ...
  Family  
  Genus  
Least general; most specific Species  
This hierarchy has evolved from a scheme first developed by the Swedish naturalist, Caroli Linnaeus, and published by him in his great work, Systema Naturae (1775 ??????). (<href=../Misc/TaxExa.html>More examples.)

biospecies vs. morphospecies

Phylogenetic Meaning of the Hierarchy

In general, the higher taxonomic levels reflect more ancient ("deeper") relationships in the evolution of organisms. Employing the useful metaphor of a family tree, it is intuitively reasonable to suppose that the cat and dog family branches diverged from one another before the different kinds of cats (or dogs) began to separate as twigs on their respective branches.

Divergence precedes diversification.

However, whereas the hierarchy may indicate the sequence in which various groups became differentiated, it tells nothing about the timing. Using our previous example, we can only say that lions and tigers became distinct from one another after the cat/dog schism; we cannot say how long ago either event took place and, in particular, we cannot say that lions and tigers separated at the same time as dingos and wolves.

                                    *** Lion

     *** Felidae (cats) ***

     *                              *** Tiger

***

     *                               *** Dingo

     ** Canidae (dogs) ***

                                    *** Wolf

There are further complications also. Even supposing that we have a perfect understanding of how organisms evolved, which of course we do not, it must be remembered that taxonomic names are primarily defined by morphological criteria rather than phylogeny. Thus, although birds and mammals arose as subgroups within the reptiles, they are both accorded the status of 'class' – the same taxonomic rank as reptiles themselves – rather than some subordinate rank within the Reptilia. If, as is generally believed, all life is descended from a single (or very few) common ancestor, such a compromise is necessary to avoid an unmanageably large number of taxonomic levels. [= xyz]
coarse level "shape"

Remaining Difficulties

If we had understood modern evolutionary synthesis during Linnaeus’ time, it is possible we would not have adopted the “binomial” convention; we would have been influenced by the knowledge that phylogenetic groupings occur at variable levels and no two are strictly comparable. Thus, the point where one draws the line between a generic distinction and a familial distinction is more or less arbitrary and is unlikely to be consistent between different lineages: Man classifies, Nature does not. Only the biospecies concept has an objective definition – can these two organisms produce viable offspring? – and even that is by no means the black-and-white distinction one might think. (What if the F2 generation is infertile? How does one account for obligate symbiotes? And, of course, the whole concept is inapplicable to any fossil taxa.)

Two further criticisms may be levelled in respect to the Linnaean hierarchy. The first criticism is that its use takes for granted a branched topology of relationships. This may be true for very large segments of the phylogenetic history of living beings, but it is definitely not true in several instances. First, the very origin of the eukaryotic cell, hence an event at the root of a disproportionately major branch of the phylogenetic tree, is currently explained as a symbiotic event, that is, as an event determining a cluster of anastomoses among the oldest branches of the tree of life. Second, anastomoses of branches of the phylogenetic tree are produced by any successful event of hybridization, which is possibly rare in animals but is certainly common in plants (at least in some groups). In all these instances, reducing the real topology of phylogeny to the conventional branched topology of the Linnean hierarchy is hardly ‘natural’.
The second criticism of the Linnaean hierarchy comes from cladistics in particular. The problem is that a phylogenetic reconstruction may only allow for the identification of nesting relationships, but cannot offer any ground to the recognition of absolute ranks. For instance, the brown bear (Ursus arctos) will turn out to be a terminal twig of the bear family (Ursids), this being in turn a branch of the Carnivores, which are nested into a larger branch Mammals, and so on. However, nothing justifies giving the same rank (say, ordinal) to Carnivores and Rodents, or – outside Mammals – to Galliforms and Coleoptera. [= xyz]
What matters more is the inadequacy of the formal Linnaean hierarchy to express the relationships of the clades in the system. This is currently a matter of dispute within the systematic community, especially with regard to what remains of the third school, known as the school of evolutionary systematics, whose principles are traditionally identified with those of E. Mayr and George Gaylord Simpson (1902–1984). According to this school, classification must be rooted in evolution, but the relevant evolutionary information must not be limited to genealogy (phylogenetic relationships) but also extended to adaptation. Accordingly, symplesiomorphies are not discarded as noninformative and paraphyletic groups are retained. As practical examples of the contrast between the two schools, two well-known groups that are clearly, or quite probably, paraphyletic and should therefore be discarded, or re-defined according to cladistic criteria, are Reptiles (should include Birds) and Dicotyledons (should include Monocotyledons, thus virtually becoming the same as Angiosperms).
All of that notwithstanding, we are stuck with the Linnean naming convention which, for all its faults, succeeds in providing a useful shorthand for identifying taxa.

Morphology vs. Genomics

"[W]hile comparitive molecular data (only available in the last few decades) have helped, they have not proved as unambiguous as we had hoped. Molecules, like morphologies, vary in their evolutionary rates and are subject to parallel and convergent evolution: and in consequence different molecules often suggest different phylogenies, just as do different morphological characters" (Arthur 1997, p. 53).

- describe the saturation problem

The most commonly used molecule is 18S rRNA, comprising about 1800 base pairs, because it is a slowly evolving molecule. Slow evolution is a prerequisite for probing very ancient phylogenetic events, to avoid the saturation problem. However, this same property makes the molecule unsuited for distinguishing events which occurred close together, perhaps during a rapid radiation. An possible example of this problem is found among annelids and molluscs; analyses which include many representatives of both phyla show a complete mix of the two groups. (Echinoderms, conversely, always appear as a monophyletic group, suggesting the modern forms represent a single lineage which diverged long ago, accumulating many unique mutations.)

Further Reading: Nielsen 2001, Chapter 57.

Historical Development

The historical development of taxonomic concepts did not proceed all at once, or even linearly. Approximate notions of animal and plant kingdoms date back to prehistoric times; Linnaeus defined genera and species

??? but not higher ranks

in the mid-1700s; and yet the three superkingdoms – the broadest division of living things – were not recognised until the late twentieth century.

Recognizing and naming species, however, does not exhaust the performance of folk taxonomies. Explicitly or not, these also include an element of hierarchy. That is, the basic named units (let us say, the species) are grouped into more general kinds, e.g. winged animals, scaly animals, etc., or legumes, lilies, etc. These ‘genera’ may be grouped, in turn, into still more general kinds, e.g. land animals, water animals, or herbs, trees, mushrooms. Up to five hierarchically nested ranks can be recognized in the most developed folk taxonomies.

Five main kinds of animals (insects, scaly animals, shelly animals, animals with feathers, animals with fur) were recognized by the Chinese pharmacologist Li Che-Chen (1518–1593)

Efforts to describe plants resulted in a tremendous increase in the number of known plant species: from the 500 species illustrated by Leonhart Fuchs (1501–1556) in De historia stirpium (1542) to the more than 6000 described by Gaspard Bauhin (1560–1624) in Pinax theatri botanici (1623) to the 18 655 listed by John Ray (1627–1705) in Methodus plantarum nova (1682).

Ray, who worked extensively on both plants and animals, observed that species can be distinguished from simple varieties in that species, but not varieties, breed indefinitely true; that is, their distinctive characters are retained from one generation to the next. He also made a valuable contribution by noting that classification should proceed upwards, rather than downwards: that is, the naturalist should begin by describing and diagnosing species, then grouping these into genera, and finally grouping genera into still more extensive groups.

The first half of the eighteenth century was dominated by the classification of plants offered in his Institutiones rei herbariae (1700) by Joseph Pitton the Tournefort (1656–1708), who arranged 698 genera in 122 sections in 22 classes. This classification was later overturned by Carolus Linnaeus (1707–1778), whose major treatises were Species plantarum and Systema naturae. Both works 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 (see below).

A critical contribution towards the future developments of biological systematics was provided by Georges-Louis Leclercq, comte de Buffon (1707–1788), who suggested a biological, i.e. functional, definition of species. In his concept, a species is a reproductive community: members of this community may freely interbreed, thus generating fertile offspring, whereas members of different species, even if similar, cannot interbreed or, if they can, only generate sterile hybrids, such as the mules and hinnies obtained by crosses between horse and donkey.

During this time there was much debate about the possibility of developing a natural, i.e. nonarbitrary, system of living beings. This possibility gained support with the development of evolutionary thinking. The otherwise mysterious ‘affinities’ between species could then be explained by common descent. In due course the reconstruction of phylogeny (genealogical relationships) become the necessary background for any serious systematic endeavour.

The phylogenetic (or cladistic) school largely identified itself, at the beginning, with Hennig’s manifesto Phylogenetic Systematics (1966). With Willi Hennig (1913–1976), the reconstruction of phylogeny becomes the primary aim of the systematist. Phylogenetic relationships are expressed by tree-like representations called cladograms. To reconstruct phylogeny, only shared derived features (synapomorphies) are informative, whereas shared primitive features (symplesiomorphies) are not. Synapomorphies identify natural units (monophyletic taxa or clades), whereas symplesiomorphies identify ‘incomplete’ groups (paraphyletic taxa or grades). Methods have been developed, since Hennig, both for the identification of the polarity of character states (primitive or plesiomorphic versus derived or apomorphic) and for the reconstruction of phylogeny from a matrix of polarized character states. Only monophyletic taxa are accepted by cladists. Strictly speaking, what is obtained by the hierarchical arrangement of nested clades should be called a system, rather than a classification.

Rules of Taxonomy

“[T]he rules for formal nomenclature require designation of types, which permanently delimit, by their measurable properties, that which must be included within the boundaries of the taxon; descriptions, which, unlike the types, can be altered (= emended); and, for fossils, illustrations” (Traverse 1996, p. 11).

The Codes

No rule seemed to be necessary at the time of Bauhin, Ray or Linnaeus, but this soon changed after the proliferation of systematic works directly or indirectly inspired by Linnaeus. Early serious efforts in this direction in zoology were the so-called Strickland’s Code (1842) and the Règles internationales de la nomenclature zoologique issued in 1905; in botany, rules were laid out in Alphonse de Candolle’s (1806–1893) Lois de la nomenclature botanique (1867).

Today, biological nomenclature is governed by the following codes:
  • International Code of Zoological Nomenclature (ICZN) (4th edn, 1999)
  • International Code of Botanical Nomenclature (ICBN) (‘Tokyo Code’, 1994)
  • International Code of Nomenclature of Bacteria (ICNB) (1990).

There are also an International Code of Nomenclature for Cultivated Plants (current edition, 1995) and a Classification and Nomenclature of Viruses, as Fifth Report of the International Committee on Taxonomy of Viruses (1991).

Several times, beginning with the 1840s and finishing with the 1990s, there have been efforts towards devising a single code which would rule the nomenclature of all living beings, but no workable result has been yet achieved.

"It is occasionally suggested, especially because of problems with protists (see discussion in Patterson & Larson 1991), that there should be just one nomenclatural code, and that would have seemed rational to Linnaeus. The differences between the two major codes, the ICBN and ICZN, are not so great as to make a unification impossible, but the prospect is unlikely. Indeed, there always have been pressures to multiply codes, resulting already, for example, in a separate code for bacteria" (Traverse 1996, p. 18).
Ref to Brochu & Sumrall 2001, Ghiselin 1984, Rowe 1986, and to the proposed PhyloCode of Cantino & de Queiroz 2000.

References

Arthur, Wallace 1997: The Origins of Animal Bodyplans. Cambridge Press, London.

Brochu, C.A.; Sumrall, C.D. 2001: Phylogenetic nomenclature and paleontology. Journal of Paleontology 75: 754-757.

Cantino, P.D. de Queiroz, K. 2000: PhyloCode: A phylogenetic code of biological nomenclature. [http://www.ohiou.edu/phylocode/]

Brown, James R. 2002: Universal Tree of Life. In Encyclopedia of Life Sciences. Nature Publishing Group, Macmillan.

Ghiselin, M.T. 1984: "Definition," "character," and other equivocal terms. Systematic Zoology 33: 104-110.

Knoll, A.H. 1996: Chapter 4. Archean and Proterozoic Paleontology. In Jansonius, J.; McGregor, D.C. (eds.) 1996: Paleontology: Principles and Applications. American Association of Stratigraphic Palynologists Foundation, v. 1, pp. 51-80.

Rowe, T. 1986: Definition and diagnosis in the phylogenetic system. Systematic Zoology 36: 208-211.

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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