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Scientific classification or biological classification is how biologists group and categorize extinct and living species of organisms. Scientific classification can also be called scientific taxonomy, but should be distinguished from folk taxonomy, which lacks scientific basis. Modern classification has its root in the work of Carolus Linnaeus, who grouped species according to shared physical characteristics. These groupings have been revised since Linnaeus 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. Scientific classification belongs to the science of taxonomy or biological systematics.

Early systems 

The earliest known system of classifying forms of life comes from the Greek philosopher Aristotle, who classified all living organisms known at that time as either a plant or an animal. He further classified animals based on their means of transportation (air, land, or water). In 1172 Ibn Rushd (Averroes), who was a judge (Qadi) in Seville, translated and abridged Aristotle's book de Anima (On the Soul) into Arabic. His original commentary is now lost, but its translation into Latin by Michael Scot survives. 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 next brought to hand descriptions and specimens of many novel forms of animal life. 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[1] 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, or method. By method they meant 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 polytipic genera. Linnaeus Two years after John Ray's death, Carolus Linnaeus (1707–1778) was born. His great work, the Systema Naturae, ran through twelve editions during his lifetime (1st ed. 1735). 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 ranks; see rank (botany) and rank (zoology).

Modern developments 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, is currently under development, intended to deal with clades rather than taxa. 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 (sometimes Monera). A small minority of scientists add Archaea as a sixth kingdom but do not accept the domain method.

Examples The usual classifications of five species follow: the fruit fly so familiar in genetics laboratories (Drosophila melanogaster), humans (Homo sapiens), the peas used by Gregor Mendel in his discovery of genetics (Pisum sativum), the "fly agaric" mushroom Amanita muscaria, and the bacterium Escherichia coli. The eight major ranks are given in bold; a selection of minor ranks are given as well.

 

Rank Fruit fly Human Pea Fly Agaric E. coli
Domain Eukarya Eukarya Eukarya Eukarya Eubacteria
Kingdom Animalia Animalia Plantae Fungi Monera
Phylum or Division Arthropoda Chordata Magnoliophyta Basidiomycota Eubacteria
Subphylum or subdivision Hexapoda Vertebrata Magnoliophytina Hymenomycotina  
Class Insecta Mammalia Magnoliopsida Homobasidiomycetae Proteobacteria
Subclass Pterygota Eutheria Magnoliidae Hymenomycetes Gammaproteobacteria
Order Diptera Primates Fabales Agaricales Enterobacteriales
Suborder Brachycera Haplorrhini Fabineae Agaricineae  
Family Drosophilidae Hominidae Fabaceae Amanitaceae Enterobacteriaceae
Subfamily Drosophilinae Homininae Faboideae Amanitoideae  
Genus Drosophila Homo Pisum Amanita Escherichia
Species D. melanogaster H. sapiens P. sativum A. muscaria E. coli

Notes:

bulletHigher taxa and especially intermediate taxa are prone to revision as new information about relationships is discovered. For example, the traditional classification of primates (class Mammalia — subclass Theria — infraclass Eutheria — order Primates) is challenged by new classifications such as McKenna and Bell (class Mammalia — subclass Theriformes — infraclass Holotheria — order Primates). See mammal classification for a discussion. These differences arise because there are only a small number of ranks available and a large number of branching points in the fossil record.
bulletWithin species further units may be recognised. Animals may be classified into subspecies (for example, Homo sapiens sapiens, modern humans) or morphs (for example Corvus corax varius morpha leucophaeus, the Pied Raven). Plants may be classified into subspecies (for example, Pisum sativum subsp. sativum, the garden pea) or varieties (for example, Pisum sativum var. macrocarpon, snow pea), with cultivated plants getting a cultivar name (for example, Pisum sativum var. macrocarpon 'Snowbird'). Bacteria may be classified by strains (for example Escherichia coli O157:H7, a strain that can cause food poisoning).
bulletAn easy way to remember the order of classification is to remember the sentence "Kings Play Chess On Fancy Glass Seats." It stands for Kingdom, Phylum, Class, Order, Family, Genus and Species.

 

Terminations of names

Taxa above the genus level are often given names based on the type genus, with a standard termination. The terminations used in forming these names depend on the kingdom, and sometimes the phylum and class, as set out in the table below.

Rank Plants Algae Fungi Animals
Division/Phylum -phyta -mycota  
Subdivision/Subphylum -phytina -mycotina  
Class -opsida -phyceae -mycetes  
Subclass -idae -phycidae -mycetidae  
Superorder -anae  
Order -ales  
Suborder -ineae  
Infraorder -aria  
Superfamily -acea -oidea
Family -aceae -idae
Subfamily -oideae -inae
Tribe/Infrafamily -eae -ini
Subtribe -inae -ina
bulletAtran, S. Cognitive foundations of natural history: towards an anthropology of science. Cambridge: Cambridge Univ. Press. 1990. xii+360 p. ISBN 0521372933
bulletLarson, J. L. Reason and experience. The representation of Natural Order in the work of Carl von Linne. Berkeley: Univ. of California Press. 1971. VII+171 p.
bulletStafleau, F. A. Linnaeus and the Linnaeans. The spreading of their ideas in systematic botany, 1753-1789. Utrecht: Oosthoek. 1971. xvi+386 p.


TAXONOMY

Taxonomy (from Greek verb τασσεῖν or tassein = "to classify" and νόμος or nomos = law, science, cf "economy") was once only the science of classifying living organisms (alpha taxonomy)

Taxonomy, sometimes alpha taxonomy, is the science of finding, describing and naming organisms, thus giving rise to taxa.


* In today's usage, Taxonomy (as a science) deals with finding, describing and naming organisms. This science is supported by institutions holding collections of these organisms, with relevant data, carefully curated: such institutes include Natural History Museums, Herbaria and Botanical Gardens.
* Systematics (as a science) deals with the relationships between taxa, especially at the higher levels. These days systematics is greatly influenced by data derived from DNA from mitochondria and chloroplasts. This is sometimes known as molecular systematics and is doing well, likely at the expense of taxonomy (Wheeler, 2004).

Cladistics is a branch of biology that determines the evolutionary relationships between organisms based on derived similarities. It is the most prominent of several forms of phylogenetic systematics, which study the evolutionary relationships between organisms. Cladistics is a method of rigorous analysis, using "shared derived traits" (synapomorphies: see below) of the organisms being studied. Cladistic analysis forms the basis for most modern systems of biological classification, which seek to group organisms by evolutionary relationships. In contrast, phenetics groups organisms based on their overall similarity, while approaches that are more traditional tend to rely on key characters (morphology). The word cladistics is derived from the ancient Greek ??????, klados, "branch."

As the end result of a cladistic analysis, treelike relationship-diagrams called "cladograms" are drawn up to show different hypotheses of relationships. A cladistic analysis can be based on as much or as little information as the researcher selects. Modern systematic research is likely to be based on a wide variety of information, including DNA-sequences (so called "molecular data"), biochemical data and morphological data.

In a cladogram, all organisms lie at the leaves, and each inner node is ideally binary (two-way). The two taxa on either side of a split are called sister taxa or sister groups. Each subtree, whether it contains one item or a hundred thousand items, is called a clade. A natural group has all the organisms contained in any one clade that share a unique ancestor (one which they do not share with any other organisms on the diagram) for that clade. Each clade is set off by a series of characteristics that appear in its members, but not in the other forms from which it diverged. These identifying characteristics of a clade are called synapomorphies (shared, derived characters). For instance, hardened front wings (elytra) are a synapomorphy of beetles, while circinate vernation, or the unrolling of new fronds, is a synapomorphy of ferns.

Willi Hennig (1913-1976) is widely regarded as the founder of cladistics.

 

Biological systematics is the study of the diversity of life on the planet earth, both past and present, and the relationships among living things through time. Systematics, in other words, is used to understand the evolutionary history of life on earth.

The term "systematics" is sometimes used synonymously with "taxonomy" and may be confused with "scientific classification." However, taxonomy is properly the describing, identifying, classifying, and naming of organisms, while "classification" is focused on placing organisms within groups that show their relationships to other organisms. All of these biological disciplines can be involved with extinct and extant organisms. However, systematics alone deals specifically with relationships through time, requiring recognition of the fossil record when dealing with the systematics of organisms.

Systematics uses taxonomy as a primary tool in understanding organisms, as nothing about an organism's relationships with other living things can be understood without it first being properly studied and described in sufficient detail to identify and classify it correctly. Scientific classifications are aids in recording and reporting information to other scientists and to laymen. The systematist, a scientist who specializes in systematics, must, therefore, be able to use existing classification systems, or at least know them well enough to skillfully justify not using them.

Phenetic systematics involves clarifying the biodiversity of earth through time by using the morphology and physiology of the organisms, while phylogenetic systematics, also called cladistics, uses apomorphies, or evolutionarily novel characteristics, to group earth's various organisms and their relationships through time. Today systematists generally make extensive use of molecular genetics and computer programs to study organisms.

Systematics is fundamental to biology because it is the foundation for all studies of organisms, by showing how any organism relates to other living things.

Systematics is also of major importance in understanding conservation issues because it attempts to explain the earth's biodiversity and could be used to assist in allocating limited means to preserve and protect endangered species, by looking at, for example, the genetic diversity among various taxa of plants or animals and deciding how much of that it is necessary to preserve.


The living world consists of millions of species of organisms. These present enormous diversity ranging from micro-organisms to the highest evolved plants and animals. The knowledge about all these organisms will be highly confusing, meaningless and useless if they are not properly identified and arranged systematically.

The systematic arrangement of properly identified and named organisms is called classification, systematics or taxonomy. (taxis = arrangement, nomos = order or law)


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Cladistics
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This cladogram shows the relationship among various insect groups.
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This cladogram shows the relationship among various insect groups.
This representation emphasises that cladograms are trees.
Enlarge
This representation emphasises that cladograms are trees.

Cladistics is a branch of biology that determines the evolutionary relationships between organisms based on derived similarities. It is the most prominent of several forms of phylogenetic systematics, which study the evolutionary relationships between organisms. Cladistics is a method of rigorous analysis, using "shared derived traits" (synapomorphies: see below) of the organisms being studied. Cladistic analysis forms the basis for most modern systems of biological classification, which seek to group organisms by evolutionary relationships. In contrast, phenetics groups organisms based on their overall similarity, while approaches that are more traditional tend to rely on key characters (morphology). The word cladistics is derived from the ancient Greek ??????, klados, "branch."

As the end result of a cladistic analysis, treelike relationship-diagrams called "cladograms" are drawn up to show different hypotheses of relationships. A cladistic analysis can be based on as much or as little information as the researcher selects. Modern systematic research is likely to be based on a wide variety of information, including DNA-sequences (so called "molecular data"), biochemical data and morphological data.

In a cladogram, all organisms lie at the leaves, and each inner node is ideally binary (two-way). The two taxa on either side of a split are called sister taxa or sister groups. Each subtree, whether it contains one item or a hundred thousand items, is called a clade. A natural group has all the organisms contained in any one clade that share a unique ancestor (one which they do not share with any other organisms on the diagram) for that clade. Each clade is set off by a series of characteristics that appear in its members, but not in the other forms from which it diverged. These identifying characteristics of a clade are called synapomorphies (shared, derived characters). For instance, hardened front wings (elytra) are a synapomorphy of beetles, while circinate vernation, or the unrolling of new fronds, is a synapomorphy of ferns.

Willi Hennig (1913-1976) is widely regarded as the founder of cladistics.
Contents
[show]

    * 1 Definitions
    * 2 Cladistic methods
    * 3 Cladistic classification
    * 4 See also
    * 5 References
    * 6 External links

[edit] Definitions

A character state (see below) that is present in both the outgroups (the nearest relatives of the group, that are not part of the group itself) and in the ancestors is called a plesiomorphy (meaning "close form", also called ancestral state). A character state that occurs only in later descendants is called an apomorphy (meaning "separate form", also called the "derived" state) for that group. The adjectives plesiomorphic and apomorphic are used instead of "primitive" and "advanced" to avoid placing value-judgments on the evolution of the character states, since both may be advantageous in different circumstances. It is not uncommon to informally refer to a collective set of plesiomorphies as a ground plan for the clade or clades they refer to.

Several more terms are defined for the description of cladograms and the positions of items within them. A species or clade is basal to another clade if it holds more plesiomorphic characters than that other clade. Usually a basal group is very species-poor as compared to a more derived group. It is not a requirement that a basal group is present. For example when considering birds and mammals together, neither is basal to the other: both have many derived characters.

A clade or species located within another clade can be described as nested within that clade.

Cladistic methods

A cladistic analysis is applied to a certain set of information. To organize this information a distinction is made between characters, and character states. Consider the color of feathers, this may be blue in one species but red in another. Thus, "red feathers" and "blue feathers" are two character states of the character "feather-color."

The researcher decides which character states were present before the last common ancestor of the species group (plesiomorphies) and which were present in the last common ancestor (synapomorphies) by considering one or more outgroups. An outgroup is an organism that is considered not to be part of the group in question, but is closely related to the group. This makes the choice of an outgroup an important task, since this choice can profoundly change the topology of a tree. Note that only synapomorphies are of use in characterising clades.

Next, different possible cladograms are drawn up and evaluated. Clades ideally have many "agreeing" synapomorphies. Ideally there is a sufficient number of true synapomorphies to overwhelm homoplasies caused by convergent evolution (i.e. characters that resemble each other because of environmental conditions or function, not because of common ancestry). A well-known example of homoplasy due to convergent evolution is the character wings. Though the wings of birds and insects may superficially resemble one another and serve the same function, each evolved independently. If a bird and an insect are both accidentally scored "POSITIVE" for the character "presence of wings", a homoplasy would be introduced into the dataset, and this gives a false picture of evolution.

Many cladograms are possible for any given set of taxa, but one is chosen based on the principle of parsimony: the most compact arrangement, that is, with the fewest character state changes (synapomorphies), is the hypothesis of relationship we tentatively accept (see Occam's razor for more on the principle of parsimony). Though at one time this analysis was done by hand, computers are now used to evaluate much larger data sets. Sophisticated software packages such as PAUP* allow the statistical evaluation of the confidence we have in the veracity of the nodes of a cladogram.

As DNA sequencing has become cheaper and easier, molecular systematics has become a more and more popular way to reconstruct phylogenies. Using a parsimony criterion is only one of several methods to infer a phylogeny from molecular data; maximum likelihood and Bayesian inference, which incorporate explicit models of sequence evolution, are non-Hennigian ways to evaluate sequence data. Another powerful method of reconstructing phylogenies is the use of genomic retrotransposon markers, which are thought to be less prone to the reversion and convergence that plagues sequence data.

Ideally, morphological, molecular and possibly other (behavioral etc.) phylogenies should be combined: none of the methods is "superior", but all have different intrinsic sources of error. For example, character convergence (homoplasy) is much more common in morphological data than in molecular sequence data, but character reversions are more common in the latter (see long branch attraction).

Cladistics does not assume any particular theory of evolution, only the background knowledge of descent with modification. Thus, cladistic methods can be, and recently have been, usefully applied to non-biological systems, including determining language families in historical linguistics and the filiation of manuscripts in textual criticism.

Cladistic classification
Three ways to define a clade for use in a cladistic taxonomy.Node-based: the most recent common ancestor of A and B and all its descendants.Stem-based: all descendants of the oldest common ancestor of A and B that is not also an ancestor of Z.Apomorphy-based: the most recent common ancestor of A and B possessing a certain apomorphy (derived character), and all its descendants.
Three ways to define a clade for use in a cladistic taxonomy.
Node-based: the most recent common ancestor of A and B and all its descendants.
Stem-based: all descendants of the oldest common ancestor of A and B that is not also an ancestor of Z.
Apomorphy-based: the most recent common ancestor of A and B possessing a certain apomorphy (derived character), and all its descendants.

A recent trend in biology since the 1960s, called cladism or cladistic taxonomy, requires taxa to be clades. In other words, cladists argue that the classification system should be reformed to eliminate all non-clades. In contrast, other taxonomists insist that groups reflect phylogenies and often make use of cladistic techniques, but allow both monophyletic and paraphyletic groups as taxa.

A monophyletic group is a clade, comprising an ancestral form and all of its descendants, and so forming one (and only one) evolutionary group. A paraphyletic group is similar, but excludes some of the descendants that have undergone significant changes. For instance, the traditional class Reptilia excludes birds even though they evolved from the ancestral reptile. Similarly, the traditional Invertebrates are paraphyletic because Vertebrates are excluded, although the latter evolved from an Invertebrate.

A group with members from separate evolutionary lines is called polyphyletic. For instance, the once-recognized Pachydermata was found to be polyphyletic because elephants and rhinoceroses arose from non-pachyderms separately. Evolutionary taxonomists consider polyphyletic groups to be errors in classification, often occurring because convergence or other homoplasy was misinterpreted as homology.

Following Hennig, cladists argue that paraphyly is as harmful as polyphyly. The idea is that monophyletic groups can be defined objectively, in terms of common ancestors or the presence of synapomorphies. In contrast, paraphyletic and polyphyletic groups are both defined based on key characters, and the decision of which characters are of taxonomic import is inherently subjective. Many argue that they lead to "gradistic" thinking, where groups advance from "lowly" grades to "advanced" grades, which can in turn lead to teleology. In evolutionary studies, teleology is usually avoided because it implies a plan that cannot be empirically demonstrated.

Going further, some cladists argue that ranks for groups above species are too subjective to present any meaningful information, and so argue that they should be abandoned. Thus they have moved away from Linnaean taxonomy towards a simple hierarchy of clades. The validity of this argument hinges crucially on how often in evolution gradualist near-equilibria are punctuated. A quasi-stable state will result in phylogenies, which may be all but unmappable onto the Linnaean hierarchy, whereas a punctuation event that balances a taxon out of its ecological equilibrium is likely to lead to a split between clades that occurs in comparatively short time and thus lends itself readily for classification according to the Linnaean system.

Other evolutionary systematists argue that all taxa are inherently subjective, even when they reflect evolutionary relationships, since living things form an essentially continuous tree. Any dividing line is artificial, and creates both a monophyletic section above and a paraphyletic section below. Paraphyletic taxa are necessary for classifying earlier sections of the tree – for instance, the early vertebrates that would someday evolve into the family Hominidae cannot be placed in any other monophyletic family. They also argue that paraphyletic taxa provide information about significant changes in organisms' morphology, ecology, or life history – in short, that both taxa and clades are valuable but distinct notions, with separate purposes. Many use the term monophyly in its older sense, where it includes paraphyly, and use the alternate term holophyly to describe clades (monophyly in Hennig's sense). As an unscientific rule of thumb, if a distinct lineage that renders the containing clade paraphyletic has undergone marked adaptive radiation and collected many synapomorphies - especially ones that are radical and/or unprecedented -, the paraphyly is usually not considered a sufficient argument to prevent recognition of the lineage as distinct under the Linnaean system (but it is by definition sufficient in phylogenetic nomenclature). For example, as touched upon briefly above, the Sauropsida ("reptiles") and the Aves (birds) are both ranked as a Linnaean class, although the latter are a highly derived offshoot of some forms of the former which themselves were already quite advanced.

A formal code of phylogenetic nomenclature, the PhyloCode, is currently under development for cladistic taxonomy. It is intended for use by both those who would like to abandon Linnaean taxonomy and those who would like to use taxa and clades side by side. In several instances (see for example Hesperornithes) it has been employed to clarify uncertainties in Linnaean systematics so that in combination they yield a taxonomy that is unambiguously placing the group in the evolutionary tree in a way that is consistent with current knowledge.
a taxon is usually assigned to a rank in a hierarchy. The basic rank is that of species, and if an organism is named it most often will receive a species name. The next most important rank is that of genus: if an organism is given a species name it will at the same time be assigned to a genus, as the genus name is part of the species name. Of the botanical names used by Linnaeus only names of genera, species and varieties are still used. The third-most important rank, although it was not used by Linnaeus, is that of family.


Thus, taxonomy is a branch of biology which deals with collection of organisms, their identification, nomenclature and systematic grouping or classification into various categories. This is done on the basis of similarities and differences of their morphological, anatomical, cytological, genetical, physiological, biochemical, developmental and other characteristics.

The similarities of characteristics between species or groups of species indicate their relationship. This is also gives us some idea about their phylogeny (i.e. their evolutionary history).

The classification of plants into various groups is called plant taxonomy or systematic botany. Similarly, classification of animals is called animal taxonomy or systematic zoology.

The original concept of species has undergone a considerable change during the progress of taxonomy. John Ray (1627-1705) was the first to distinguish genus and species. However, the clear morphological concept of species was first given by Linnaeus (1707-1778). Later on, Darwin proposed the biological concept of species. The concept was further modified by Ernst Meyr.

Morphological concept of species by Linnaeus. A species is the group of individual which resemble each other in most major morphological (vegetative and reproductive) characteristics.


Biological concept of species by Darwin. In addition to morphology, the biological concept also takes into consideration ecology, geography, cytology, physiology, behavior, etc.

According to the biological concept, a species is a group of individuals which resemble each other in morphological, physiological, biochemical, and behavioral characteristics. These individuals are capable of breeding with each other under natural conditions, but are unable to breed successfully with members of other species.

Thus, species is a group of fertile organisms that can interbreed and produce fertile offspring only among themselves.

The recent trend is to consider species as the groups of actually or potentially interbreeding natural populations of closely resembling individuals (Ernst Meyr).

A species is considered to be the smallest, most basic unit of classification in most of the systems. It was thought to be an indivisible, stable and static unit (taxon). However, in modern taxonomy, sub-divisions of species, such as sub-species and populations, have been created which aid in our understanding through classification.

 

Taxa and Categories

(1) Taxa (Singular: Taxon): A taxon is the taxonomic group of any rank in the system of classification (H.J.Lam, 1948). For example, in plant kingdom, each one of the following such as, angiosperms, dicotyledons, polypetalae, Malvaceae, Hibiscus esculentus, etc. represents a taxonomic group i.e. a taxon. A taxon may be a very large group such as a Division (e.g. angiosperms), or it can be a very small group such as a species (e.g. Hibiscus esculentus).

(2) Categories (Singular: Category): In the system of classification, the various taxa are assigned definite ranks or positions according to their taxonomic status. Each such taxonomic rank is called the taxonomic category. The various major categories in the classification of plant kingdom are Kingdom, Division (Phylum), Class, Series, Order, Family, Genus and Species.


The difference between the taxon and the category should be clearly understood. For example, when we say "Division- Angiosperms", 'Division' represents the taxonomic category while 'angiosperms' represents the taxon. Thus, a taxon is a group of organisms (living beings), whereas a category only indicates the rank or status of the taxon in the systematic hierarchy.

Arranging various taxonomic categories in their proper order on the basis of their taxonomic ranks is called taxonomic hierarchy (systematic hierarchy). In this hierarchy, the kingdom represents the category of highest rank while the species is the category of the basic rank.

Following is an example of the taxonomic hierarchy representing the methodology of classifying a plant and an animal in a scientific manner.

A broad scheme of ranks in hierarchical order:

    Domain
    Kingdom
    Phylum (animals or plants) or Division (plants)
    Class
    Order
    Family
    Genus
    Species
    Subspecies 
The prefix super- indicates a rank above, the prefix sub- indicates a rank below. In zoology the prefix infra- indicates a rank below sub-

 

Binomial Nomenclature

The system of giving a scientific name to each properly identified plant or animal is called nomenclature.

A system of nomenclature of plants and animals in which each scientific name consists of two parts or sub-names is called the system of binomial nomenclature.

Thus according to this system the scientific name of sunflower is Helianthus annuus and that of man is Homo sapiens.

In the above names, the first part of the name (i.e. Helianthus or Homo) represents the name of the genus (generic name). The second part of the name (i.e. annuus or sapiens) represents the name of the species (specific name).

This system of binomial nomenclature was introduced by Carolus Linnaeus in 1753 in his book Species Plantarum.

The system follows certain rules, such as :

  1. The scientific name must be in Greek or Latin language.

  2. Genetic name should come first and must begin with a capital letter.

  3. The same name should not be used for two or more species under the same genus.

  4. The scientific name must be either underlined or written in italics.

  5. The name of the author who first described the species should be written after the specific name (e.g. Homo sapiens Linnaeus).

Principles of Classification

While developing a system of classification of organisms, certain basic principles are observed. Some of these are as follows:

(i) Morphological criteria:

Morphology forms the primary basis for classifying organisms into various taxonomic groups or taxa. In earlier artificial systems, only one or a few morphological characters were taken into consideration (e.g. plants were classified into herbs, shrubs, trees, climbers, etc. on the basis of their habit). The sexual system proposed by Linnaeus was based mainly on the characteristics of stamens and carpels.

Later on, in the natural systems of classification (e.g. Bentham and Hooker's system of classification of plants), a large number of morphological characters were taken into consideration. As a result, classification of plant groups was more satisfactory and their arrangement was showing natural relationships with each other.

The similarities in the morphological characters are used for grouping the plants together. Because, these similarities indicate their relationships. On the other hand, differences or dissimilarities of characters are used for separating the plant groups from each other. Plant groups with greater differences are considered to be unrelated or distantly related.

For example, all flowering plants with ovules enclosed in an ovary cavity are grouped together as Division - Angiosperms whereas, the angiosperms are further classified into two classes: Dicotyledons and Monocotyledons, on the basis of differences of the characters of root system, leaf venation, flower symmetry and number of cotyledons in the embryo.

(ii) Phylogenetic considerations :

In the more recent systems of classification of plants, a greater emphasis is given on the phylogenetic arrangement of plant groups, an arrangement which is based on the evolutionary sequence of the plant groups. These systems also reflect on the genetic similarities of the plants. Some of the phylogenetic systems of classification of plants are the ones proposed by Engler and Prantle (1887-1899), Bessey (1915), Hutchinson (1926 and 1934), etc.

However, none of these or any other systems is a perfect phylogenetic system. This is because, our present knowledge of the evolutionary history of plant groups is very fragmentary and incomplete. At best, the present day systems can be described as the judicious combination of both natural and phylogenetic systems.

Modern taxonomy takes into consideration data available from all disciplines of botany for classification of plants. This helps immensely in establishing inter-relationships of various plant groups. As a result, taxonomic arrangement becomes more authentic and convincing.

(iii) Chemical taxonomy or chemotaxonomy:

is a comparatively recent discipline. Chemotaxonomy is the application of phyto-chemical data to the problems of systematic botany.

The presence and distribution of various chemical compounds in plants serve as taxonomic evidences. Nearly 33 different groups of chemical compounds have been found to be of taxonomic significance.

(iv) Numerical taxonomy :

Application of numerical methods (data) in the classification of taxonomic units is called numerical taxonomy.

Edgar Anderson (1949) was the first to make use of numerical taxonomy in the classification of flowering plants. It involves exhaustive quantitative estimation of taxonomic characters from all parts of the plant as well as from all stages in the life cycle. The numerical data thus collected for various plant groups is tabulated systematically. Computers are used for this purpose.

The main objective of numerical taxonomy is to clarify and illustrate degrees of relationship or similarity in an objective manner. This branch is becoming an indispensable aid in modern systematics.

SUMMARY - CLASSIFICATION

(1) Classification is essential for the proper study and easy reference to the immense variety of life forms.

(2) Systematics deals with identification, nomenclature and taxonomic classification of organisms.

(3) Species has a great significance as a taxonomic unit.

(4) Recent taxonomy gives more importance to sub-species and populations.

(5) In the systematic classification of organisms, various taxa are arranged in the descending order of their taxonomic categories as per the taxonomic hierarchy.

(6) Modern taxonomy makes use of the data from all branches of botany, including genetics, cytology, ecology, chemotaxonomy, numerical taxonomy, etc. in order to develop a phylogenetic system of classification of plants.

The Integrated Taxonomic Information System (ITIS) is a partnership designed to provide consistent and reliable information on the taxonomy of biological species. ITIS was originally formed in 1996 as an interagency group within the U.S. federal government, involving agencies from the Department of Commerce to the Smithsonian Institution. It has now become an international body, with Canadian and Mexican government agencies participating. The primary focus of ITIS is North American species, but many groups are worldwide and ITIS continues to collaborate with other international agencies to increase its global coverage.

ITIS provides an automated reference database of scientific and common names for species. As of December 2005, it contains over 500,000 scientific names, synonyms, and common names for terrestrial, marine, and freshwater taxa from all biological kingdoms (animals, plants, fungi, and microbes). While the system does focus on North American species, it also includes many species not found in North America, especially among birds, fishes, amphibians, mammals, many reptiles, and several invertebrate animal groups. ITIS couples each scientific name with a stable and unique taxonomic serial number TSN as the “common denominator” for accessing information on such issues as invasive species, declining amphibians, migratory birds, fishery stocks, pollinators, agricultural pests, and emerging diseases. It presents the names in a standard classification that contains author, date, distributional, and bibliographic information related to the names. In addition, common names are available through ITIS in the major official languages of the Americas (English, French, Spanish, and Portuguese). ITIS and its international partner, Species 2000, cooperate to annually produce the Catalogue of Life, a checklist and index of the world’s species. The Catalogue of Life goal is to complete the global checklist of 1.8 million species by 2011.

Of the nearly 415,660 (April 2006) scientific names in the current database, approximately 210,000 were inherited from the database formerly maintained by the National Oceanographic Data Center (NODC) of the US National Oceanic and Atmospheric Administration (NOAA). The newer material has been checked to higher standards of taxonomic credibility, and over half of the original material has been checked and improved to the same standard. For further background on ITIS and for information to help interpret what can be found therein, please see the ITIS' Data Development History and Data Quality page [1], and the Glossary of Terms Used in ITIS [2].

Biological taxonomy is not fixed, and opinions about the correct status of taxa at all levels, and their correct placement, are constantly revised as a result of new research. Many aspects of classification will always remain a matter of scientific judgement. The ITIS database is updated to take account of new research as it becomes available, and the information it yields is likely to represent a fair consensus of modern taxonomic opinion. Records within ITIS include information about how far it has been possible to check and verify them. Its information should be checked against other sources where these are available, and against the primary research scientific literature where possible.

 

The nature of plant species

Loren H. Rieseberg, Troy E. Wood1 and Eric J. Baack
Many botanists doubt the existence of plant species viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or 'units of evolution'. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few 'botanical horror stories', such as dandelions, blackberries and oaks6, 7. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera (> 80%), the correspondence of taxonomic species to these clusters is poor (< 60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom8, plant species are more likely than animal species to represent reproductively independent lineages.

Do plant species really exist? Yes, scientists say

FOR IMMEDIATE RELEASE
March 22, 2006

BLOOMINGTON, Ind. -- Notoriously "promiscuous" plants like oaks and dandelions have led some biologists to conclude plants cannot be divided into species the same way animals are.

That perception is wrong, say Indiana University Bloomington scientists in this week's Nature. Their analysis of 882 plant and animal species and 1,347 inter-species crossings -- the first large-scale comparison of species barriers in plants and animals -- showed that plant species are just as easily categorized as animal species.

The study also yielded a surprise. The hybrid offspring of different animal species are more likely to be fertile than the hybrid offspring of plant species.
Plant fantasy
Photo by: Robert Czarny
Are plant species real or imagined? Many botanists have argued that grouping plants into species is merely an exercise of convenience.
Print-Quality Photo

"We found that not only are plants just as easily subdivided into species as animals when analyzed statistically, but plants are more likely to be reproductively isolated due to hybrid sterility," said evolutionary biologist Loren Rieseberg, who led the study. "Most plant species are indeed 'real.' The problem has been that botanists have been way over-attracted to the plant species that readily hybridize and where the hybrids perpetuate themselves asexually. While it's true that dandelions and blackberries pose problems, these horror stories only make up 1 percent of the whole."

The scientists did find categorization problems with nearly half of the plant and animal species they surveyed.

Rieseberg and his co-authors, doctoral student Troy Wood and postdoctoral research associate Eric Baack, examined hundreds of peer-reviewed papers reporting the measurement of various plant and animal characteristics, or reporting on the success or failure of hybridization of plant and animal species with similar species. The scientists culled the papers for information, grouped and combined data for each given species, and then looked at how often characteristics clustered in accordance with named species.

The scientists found that while real, quantifiable clusters did exist in most groups of plants and animals, the one-to-one correspondence of species names and character clusters was quite low -- about 54 percent. One explanation for this, Rieseberg said, is that too many taxonomists are "splitters" -- they give too many species names to a single group of related organisms.

After analyzing the hybridization data, the scientists found that only 30 percent of the approximately 500 plant species they surveyed are able to produce fertile hybrids when mated with other species. By stark contrast, 61 percent of animal species surveyed are able to reproduce successfully with other species.

The hybridization of animal species is often portrayed as rare and strange, or else the result of human-forced matings, as is the case with ligers (lion-tiger hybrids) and mules (horse-ass hybrids). It is not common knowledge that many bird and fish species successfully hybridize in the wild. The scientists found that birds were most likely to produce fertile hybrids when crossed with other bird species. Ferns, of all things, were least likely to generate fertile hybrids.

Many of the hybridization papers that Rieseberg, Wood and Baack looked at reported crossings under laboratory conditions, and therefore the crossings may not accurately represent what happens in nature. For example, two species that can hybridize may not actually do so, perhaps because they exist on different continents or because they prefer to mate with members of their own species. For that reason, the percentages of plant and animal species that hybridize in the wild are likely to be lower than those reported by the scientists.

The Nature study is meant to address gaps in scientists' knowledge in two areas: the fundamental nature of species and the divisibility of plant and animal species using commonly accepted definitions of species. Debates in both areas began with the 1859 edition of Darwin's Origin of Species, and they have not yet been settled.

"These discussions should have been settled earlier, but no one bothered to summarize the relevant literature, perhaps because it is so vast," Rieseberg said.

Over the past 50 years, numerous scientific papers have been published in which species are categorized by statistical analysis of observable traits (i.e., numerical taxonomy) and/or by the ease with which species can be hybridized (i.e., breeding studies). "After going through all this literature, we realized someone just needed to compile and analyze it all," Rieseberg said.

The scientists decided to use the mass of data to see whether taxonomists were doing a good job, and whether cross-species mating in the plant kingdom is especially likely to be successful.

"The species concept debate has devolved from an empirical discussion into a philosophical one," Rieseberg said. "But this is fundamentally an empirical question. These data support the notion that species can be both units of evolution and products of evolution."

Rieseberg holds the Class of '54 Chair and is a distinguished professor of biology at IU Bloomington. Troy Wood and Eric Baack also contributed to the report. It was funded primarily by a Guggenheim Fellowship grant. Supplementary support came from the MacArthur Foundation, the National Institutes of Health and the National Science Foundation.

Paper coauthors Troy Wood and Eric Baack are available for comment. Rieseberg is away and unavailable. To speak with Wood, call 812-855-5873 or e-mail trowood@indiana.edu. To speak with Baack, call 812-855-9018 or e-mail ebaack@indiana.edu.

"The Nature of Plant Species," Nature, v. 440 (7081)

 

 

 

 

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