Biological Classification

Biological classification or scientific classification in biology, is a method by which biologists group and categorize species of organisms. Biological classification is a form of scientific taxonomy, but should be distinguished from folk taxonomy, which lacks scientific basis. Modern biological classification has its root in the work of Carolus Linnaeus, who grouped species according to shared physical characteristics. These groupings since have been revised to improve consistency with the Darwinian principle of common descent. Molecular systematics, which uses DNA sequences as data, has driven many recent revisions and is likely to continue to do so. Biological classification belongs to the science of biological systematics.

Early systems
Ancient through medieval times

Current systems of classifying forms of life descend from the thought presented by the Greek philosopher Aristotle, who published in his metaphysical and logical works the first known classification of everything whatsoever, or "being". This is the scheme that gave moderns such words as substance, species and genus and was retained in modified and less general form by Linnaeus.

Aristotle also studied animals and classified them according to method of reproduction, as did Linnaeus later with plants. Aristotle's animal classification was soon made obsolete by additional knowledge and was forgotten.


The philosophical classification is in brief as follows. Primary substance is the individual being; for example, Peter, Paul, etc. Secondary substance is a predicate that can properly or characteristically be said of a class of primary substances; for example, man of Peter, Paul, etc. The characteristic must not be merely in the individual; for example, being skilled in grammar. Grammatical skill leaves most of Peter out and therefore is not characteristic of him. Similarly man (all of mankind) is not in Peter; rather, he is in man.

Species is the secondary substance that is most proper to its individuals. The most characteristic thing that can be said of Peter is that Peter is a man. An identity is being postulated: "man" is equal to all its individuals and only those individuals. Members of a species differ only in number but are totally the same type.

Genus is a secondary substance less characteristic of and more general than the species; for example, man is an animal. Not all animals are men. It is clear that a genus contains species. There is no limit to the number of Aristotelian genera that might be found to contain the species. Aristotle does not structure the genera into phylum, class, etc., as does Linnaean classification, that development only happened in 1956.


The secondary substance that distinguishes one species from another within a genus is the specific difference. Man can thus be comprehended as the sum of specific differences (the "differentiae" of biology) in less and less general categories. This sum is the definition; for example, man is an animate, sensate, rational substance. The most characteristic definition contains the species and the next most general genus: man is a rational animal. Definition is thus based on the unity problem: the species is but one yet has many differentiae.



The very top genera are the categories. There are ten: one of substance and nine of "accidents", universals that must be "in" a substance. Substances exist by themselves; accidents are only in them: quantity, quality, etc. There is no higher category, "being", because of the following problem, which was only solved in the Middle Ages by Thomas Aquinas: a specific difference is not characteristic of its genus. If man is a rational animal, then rationality is not a property of animals. Substance therefore cannot be kind of being because it can have no specific difference, which would have to be non-being.

The problem of being occupied the attention of scholastics during the time of the Middle Ages. The solution of St. Thomas, termed the analogy of being, established the field of ontology, which received the better part of the publicity and also drew the line between philosophy and experimental science. The latter rose in the Renaissance from practical technique. Linnaeus, a classical scholar, combined the two on the threshold of the neo-classicist revival now called the Age of Enlightenment.

It's no secret that humans (with the notable exception of college students) like to keep things organized. Garages, libraries, laboratories and workshops are easier to work in if there is a system in place to keep track of things. Wrenches go in this drawer, screwdrivers go in that drawer, drills go in that cabinet. Biology is no exception. Its a lot easier to study living things if we have a system that keeps some things apart from other things. Biologists call this system taxonomy . Taxonomy took a great leap forward thanks to the efforts of an 18th century biologist named Linnaeus. What Linnaeus did was devise a system of binomial nomenclature. A hundred years later, the International Congress of Zoologists set formal rules for systematically naming things. The rules are:

1. Names must be Latin or latinized and are printed in italics. Like everything else printed in italics, they are underlined when handwritten.
2. The genus name (the Homo in Homo sapiens) is capitalized and must be a single word.
3. The species name ( sapiens in Homo sapiens) can be either a single word or a compound word (a new word made up of two words).
4. Credit for authorship of names will be given to the person who first publishes it with an accurate and recognizable description of the organism.

I won't go crazy about describing binomial nomenclature. The most important thing for this lab is yet to come. What you should know are these 4 rules. Typically, you'll see questions on quizzes or exams like, "Which one of these is the accepted name for a horse?"

1. equus cabballus
2. Equus Cabballus
3. Equus cabbalus
4. equus Caballus

Even if you didn't know the scientific name of a horse, you would know 3 is correct because the others break one of the rules.

What Linnaeus also did was systematically categorize all known organisms. Linnaeus came up with a hierachy of ways to classify plants and animals. The different levels are called taxa (plural of taxon). The different taxa are:

• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species

Kingdom is the broadest of the taxa, all animals are in Kingdom Animalia. All plants are in Kingdom Plantae. Phyla are slightly less broad. There are usually a few phyla in each kingdom. Species is the most restricted.
The easiest way to remember the different levels (I can guarantee you'll see this on one or more tests):

King Philip Came Over For Good Soup

King = Kingdom, Philip = Phylum, Came = Class, Over = Order, For = Family, Good = Genus, Soup = Species.

Renaissance through age of reason

An important advance was made by the Swiss professor, Conrad von Gesner (1516–1565). Gesner's work was a critical compilation of life known at the time.

The exploration of parts of the New World produced large numbers of new plants and animals that needed descriptions and classification. The old systems made it difficult to study and locate all these new specimens within a collection and often the same plants or animals were given different names simply because there were too many species to keep track of. A system was needed that could group these specimens together so they could be found; the binomial system was developed based on morphology with groups having similar appearances. In the latter part of the 16th century and the beginning of the 17th, careful study of animals commenced, which, directed first to familiar kinds, was gradually extended until it formed a sufficient body of knowledge to serve as an anatomical basis for classification. Advances in using this knowledge to classify living beings bear a debt to the research of medical anatomists, such as Fabricius (1537–1619), Petrus Severinus (1580–1656), William Harvey (1578–1657), and Edward Tyson (1649–1708). Advances in classification due to the work of entomologists and the first microscopists is due to the research of people like Marcello Malpighi (1628–1694), Jan Swammerdam (1637–1680), and Robert Hooke (1635–1702). Lord Monboddo (1714-1799) was one of the early abstract thinkers whose works illustrate knowledge of species relationships and who foreshadowed the theory of evolution. Successive developments in the history of insect classification may be followed on the website by clicking on succeeding works in chronological order.

Early methodists

Since late in the 15th century, a number of authors had become concerned with what they called methodus, (method). By method authors mean an arrangement of minerals, plants, and animals according to the principles of logical division. The term Methodists was coined by Carolus Linnaeus in his Bibliotheca Botanica to denote the authors who care about the principles of classification (in contrast to the mere collectors who are concerned primarily with the description of plants paying little or no attention to their arrangement into genera, etc). Important early Methodists were an Italian philosopher, physician, and botanist Andrea Caesalpino, an English naturalist John Ray, a German physician and botanist Augustus Quirinus Rivinus, and a French physician, botanist, and traveller Joseph Pitton de Tournefort.

Andrea Caesalpino (1519–1603) in his De plantis libri XVI (1583) proposed the first methodical arrangement of plants. On the basis of the structure of trunk and fructification he divided plants into fifteen "higher genera".

John Ray (1627–1705) was an English naturalist who published important works on plants, animals, and natural theology. The approach he took to the classification of plants in his Historia Plantarum was an important step towards modern taxonomy. Ray rejected the system of dichotomous division by which species were classified according to a pre-conceived, either/or type system, and instead classified plants according to similarities and differences that emerged from observation.

Both Caesalpino and Ray used traditional plant names and thus, the name of a plant did not reflect its taxonomic position (e.g. even though the apple and the peach belonged to different "higher genera" of John Ray's methodus, both retained their traditional names Malus and Malus Persica respectively). A further step was taken by Rivinus and Pitton de Tournefort who made genus a distinct rank within taxonomic hierarchy and introduced the practice of naming the plants according to their genera.

Augustus Quirinus Rivinus (1652–1723), in his classification of plants based on the characters of the flower, introduced the category of order (corresponding to the "higher" genera of John Ray and Andrea Caesalpino). He was the first to abolish the ancient division of plants into herbs and trees and insisted that the true method of division should be based on the parts of the fructification alone. Rivinus extensively used dichotomous keys to define both orders and genera. His method of naming plant species resembled that of Joseph Pitton de Tournefort. The names of all plants belonging to the same genus should begin with the same word (generic name). In the genera containing more than one species the first species was named with generic name only, while the second, etc were named with a combination of the generic name and a modifier (differentia specifica).

Joseph Pitton de Tournefort (1656–1708) introduced an even more sophisticated hierarchy of class, section, genus, and species. He was the first to use consistently the uniformly composed species names which consisted of a generic name and a many-worded diagnostic phrase differentia specifica. Unlike Rivinus, he used differentiae with all species of polytypic genera.

Modern systems
Linnaean

Two years after John Ray's death, Carolus Linnaeus (1707–1778) was born. His great work, the Systema Naturae (1st ed. 1735), ran through twelve editions during his lifetime. In this work, nature was divided into three kingdoms: mineral, vegetable and animal. Linnaeus used five ranks: class, order, genus, species, and variety.

He abandoned long descriptive names of classes and orders and two-word generic names (e. g. Bursa pastoris) still used by his immediate predecessors (Rivinus and Pitton de Tournefort) and replaced them with single-word names, provided genera with detailed diagnoses (characteres naturales), and reduced numerous varieties to their species, thus saving botany from the chaos of new forms produced by horticulturalists.

Linnaeus is best known for his introduction of the method still used to formulate the scientific name of every species. Before Linnaeus, long many-worded names (composed of a generic name and a differentia specifica) had been used, but as these names gave a description of the species, they were not fixed. In his Philosophia Botanica (1751) Linnaeus took every effort to improve the composition and reduce the length of the many-worded names by abolishing unnecessary rhetorics, introducing new descriptive terms and defining their meaning with an unprecedented precision. In the late 1740s Linnaeus began to use a parallel system of naming species with nomina trivialia. Nomen triviale, a trivial name, was a single- or two-word epithet placed on the margin of the page next to the many-worded "scientific" name. The only rules Linnaeus applied to them was that the trivial names should be short, unique within a given genus, and that they should not be changed. Linnaeus consistently applied nomina trivialia to the species of plants in Species Plantarum (1st edn. 1753) and to the species of animals in the 10th edition of Systema Naturae (1758).

By consistently using these specific epithets, Linnaeus separated nomenclature from taxonomy. Even though the parallel use of nomina trivialia and many-worded descriptive names continued until late in the eighteenth century, it was gradually replaced by the practice of using shorter proper names combined of the generic name and the trivial name of the species. In the nineteenth century, this new practice was codified in the first Rules and Laws of Nomenclature, and the 1st edn. of Species Plantarum and the 10th edn. of Systema Naturae were chosen as starting points for the Botanical and Zoological Nomenclature respectively. This convention for naming species is referred to as binomial nomenclature.


Today, nomenclature is regulated by Nomenclature Codes, which allows names divided into taxonomic ranks.

Taxonomic ranks

There are 8 main taxonomic ranks: domain, kingdom, phylum, class, order, family, genus, species.
There are slightly different ranks for zoology and for botany in biological classification.

Taxanomic ranks
				Magnorder
Domain/ Superkingdom	Superphylum/ Superdivision	Superclass		Superorder			Superfamily	Superspecies
Kingdom	Phylum/Division	Class	Legion	Order	Family	Tribe	Genus	Species
Subkingdom	Subphylum	Subclass	Cohort	Suborder	Subfamily	Subtribe	Subgenus	Subspecies
Infrakingdom/Branch	Infraphylum	Infraclass		Infraorder		Alliance		Infraspecies
	Microphylum	Parvclass		Parvorder

Evolutionary

Whereas Linnaeus classified for ease of identification, it is now generally accepted that classification should reflect the Darwinian principle of common descent.

Since the 1960s a trend called cladistic taxonomy (or cladistics or cladism) has emerged, arranging taxa in an evolutionary tree. If a taxon includes all the descendants of some ancestral form, it is called monophyletic, as opposed to paraphyletic. Other groups are called polyphyletic.

A new formal code of nomenclature, the PhyloCode, to be renamed "International Code of Phylogenetic Nomenclature" (ICPN), is currently under development, intended to deal with clades, which do not have set ranks, unlike conventional Linnaean taxonomy. It is unclear, should this be implemented, how the different codes will coexist.

Domains are a relatively new grouping. The three-domain system was first invented in 1990, but not generally accepted until later. Now, the majority of biologists accept the domain system, but a large minority use the five-kingdom method. One main characteristic of the three-domain method is the separation of Archaea and Bacteria, previously grouped into the single kingdom Bacteria (a kingdom also sometimes called Monera). Consequently, the three domains of life are conceptualized as Archaea, Bacteria, and Eukaryota (comprising the nuclei-bearing eukaryotes). A small minority of scientists add Archaea as a sixth kingdom, but do not accept the domain method.

Thomas Cavalier-Smith, who has published extensively on the classification of protists, has recently proposed that the Neomura, the clade which groups together the Archaea and Eukarya, would have evolved from Bacteria, more precisely from Actinobacteria.

Linnaeus 1735 2 kingdoms	Haeckel 1866 3 kingdoms	Chatton 1937 2 empires	Copeland 1956 4 kingdoms	Whittaker 1969 5 kingdoms	Woese et al. 1977 6 kingdoms	Woese et al. 1990 3 domains
(not treated)	Protista	Prokaryota	Monera	Monera	Eubacteria	Bacteria
					Archaebacteria	Archaea
		Eukaryota	Protista	Protista	Protista	Eukarya
Vegetabilia	Plantae			Fungi	Fungi
			Plantae	Plantae	Plantae
Animalia	Animalia		Animalia	Animalia	Animalia

Authorities (author citation)

The name of any taxon may be followed by the "authority" for the name, that is, the name of the author who first published a valid description of it. These names are frequently abbreviated: the abbreviation "L." is universally accepted for Linnaeus, and in botany there is a regulated list of standard abbreviations (see list of botanists by author abbreviation). The system for assigning authorities is slightly different in different branches of biology: see author citation (botany) and author citation (zoology). However, it is standard that if a name or placement has been changed since the original description, the first authority's name is placed in parentheses and the authority for the new name or placement may be placed after it (usually only in botany).

Globally Unique Identifiers for Names

There is a movement within the biodiversity informatics community to provide Globally Unique Identifiers in the form of Life Science Indentifiers for all biological names. This would allow authors to cite names unambiguously in electronic media and reduce the significance of errors in the spelling of names or the abbreviation of authority names. Three large nomenclatural databases (referred to as nomenclators) have already begun this process, these are Index Fungorum, International Plant Names Index and Zoo Bank. Other databases, that publish taxonomic rather than nomenclatural data, have also started using LSIDs to identify taxa. The key example of this is Catalogue of Life. The next step in integration will be when these taxonomic database include references to the nomenclatural databases using LSIDs.

References on Biological Classification

• Categories Section 5 and Metaphysics Book 6, but the terms are used in many places throughout the writings of Aristotle.
  
• See especially pp. 45, 78 and 555 of Joel Cracraft and Michael J. Donaghue, eds. (2004). Assembling the Tree of Life. Oxford, England: Oxford University Press.
  
• E. Haeckel (1866). Generelle Morphologie der Organismen. Reimer, Berlin.
  
• E. Chatton (1937). Titres et travaux scientifiques. Sette, Sottano, Italy.
  
• H. F. Copeland (1956). The Classification of Lower Organisms. Palo Alto: Pacific Books.
  
• R. H. Whittaker (1969). "New concepts of kingdoms of organisms". Science 163: 150–160.
  
• C. R. Woese, W. E. Balch, L. J. Magrum, G. E. Fox and R. S. Wolfe (1977). "An ancient divergence among the bacteria". Journal of Molecular Evolution 9: 305–311.
  
• Woese C, Kandler O, Wheelis M (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.". Proc Natl Acad Sci U S A 87 (12): 4576–9.
  
• Atran, S. (1990). Cognitive foundations of natural history: towards an anthropology of science. Cambridge, England: Cambridge University Press. xii+360 pages.
  
• Larson, J. L. (1971). Reason and experience. The representation of Natural Order in the work of Carl von Linne. Berkeley, California: University of California Press. VII+171 pages.
  
• Species 2000 & ITIS Catalogue of Life 2008
  
• Stafleau, F. A. (1971). Linnaeus and the Linnaeans. The spreading of their ideas in systematic botany, 1753-1789. Utrecht: Oosthoek. xvi+386 pages.