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 Orgafication and namesnism classi

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تاريخ التسجيل : 19/06/2010
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مُساهمةموضوع: Orgafication and namesnism classi   الثلاثاء ديسمبر 21, 2010 4:22 am


While popular names for common animals and plants are in common usage, all known life (and past life) has a strict formal name. The naming of any organism is a classification system known as Taxonomy, and its importance, and the different divisions recognised, are discussed below.

The following discussion covers:

•Taxonomy
•Relevance to Fossils
•Classifications
•Species to Orders
•Classes to Kingdoms
•Defining the Hierarchy
Taxonomy
Taxonomy is the formal classification of organisms (soils, or other entities) based on degrees of relatedness amongst those being considered.

It is more than a 'glorified form of filing', but is instead 'a fundamental and dynamic science, dedicated to exploring the causes of relationships and similarities amongst organisms'.

Popular names are convenient for common usage; but they may be incomplete, or duplicate - there are often many names for one species, and a single name can be used for different species.
To avoid this confusion, and to easily label newly-discovered organisms that will never justify a common name, all identified life (both present and past) has a strict scientific name. It may be long and cumbersome, but adheres to agreed and strict standards.
This name allows instant and exact placement of the organism within its taxonomic hierarchy (except where errors and duplications have been made, of course!).

These names are always in Latin, or are "Latinised" when new words are used. They are at all times:

•Precise and unique, and define the specific organism,
•They are international, so identical whatever language is in use (as any names are either Latin, or 'Latinised')
•All animals have received a scientific label, even if they are so rare and unknown outside a lab, that no popular name has been coined. If a new form is discovered, then its name is created by the worker who first published its description. (By convention, s/he does not name it after herself, not even after her direct supervisor,[supervisor|boss|superior?] if a student. - but this convention is often ignored). [Try to get a local e.g. of a chalk critter])
A major problem with classification is that it has, and is, changing. This is largely because of advanced techniques of molecular sequencing, which give far more details than could ever be seen from a complete organisms.
This has meant that at all levels, from species to Kingdom, the classifications are still changing - for example, that the Kingdom Monera has now been dropped.

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Relevance to Fossils
Correct identification of a fossil is a first step, and necessary before any further information about it can be found. For correct identification, sound classification and nomenclature must be used. The science of taxonomy (or systematics, as it is sometimes called) is the oldest of all biological disciplines, and the principles outlined by Carl Gustav Linnaeus (1707-1778) are still in use today, though greatly modified and extended.

The fundamental unit of taxonomy is the species, which is defined below as being a group of organisms with 'reproductive isolation' - that is, that cannot successfully breed outside the group.
This means that it is only really possible to distinguish a closely-related species if breeding habits are known. This is not always easy with living species - less than 20% of living animals are properly described as species, as the breeding habits of the remainder are not known. It is even harder with extinct animals that we know of only as fossils of the organism's hard parts (shells and skeletons).
Despite this limitation, much has been done in classifying fossils as species, based on less technically-valid criteria - mainly, their appearance. This is their morphology, or form, as most natural species tend to be composed of individuals that look the 'about the same'.

This leads to many problems, such as those of:
•size (are there two species, or are they adult and juvenile?)
•sexual dimorphism (are there two species, or are they male and female? This caused a particular problem with ammonites [link to page when written]
•stage (are there two species, or have individuals at different stages of maturity in a multi-stage specimen (as some insects, with their 4-stage life-cycle of egg --> larva --> pupa --> imago ?)
•morphological variation (are there two species, or simply sub-species and individuals that look different - there is usually a spread of morphological variation within a breeding population)
•geographical variation (are there two species, or one that has been separated and started to evolve separately, but has not yet formed two distinct species?)
•stratigraphical variation (are there two species, or individuals from different ages, the latter of which has started to evolve, but has not yet formed a new species?
An example of one such a problem in the fossil record is that of the late Devonian tree group of progymnosperms.
The progymnosperms produced, for the first time, wood that had all the characteristics of modern conifers. However, their foliage and reproductive structure that looked like that of modern ferns, not trees.
Until the wood and foliage were found together in the fossil record, the wood and foliage had therefore been considered to be from quite different plants, and had been placed in very separate divisions within the taxonomic hierarchy.
On discovery of the fossil specimens showing foliage attached to the wood (in 1960) the extinct class of progymnosperms was thus devised.

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Classifications
Animals and plants are grouped into several categories which indicate their degree of relationship, one to another.

These, starting from the general to the specific, are:

•Kingdom
•Phylum
•Class
•Order
•Family
•Genus
•Species
All taxonomic categories above the species level are to some extent artificial and subjective - and when breeding habits are not known, this applies within the species category too.
Despite this, all categories should ideally reflect evolutionary relationships.

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From specific to general:

Species to Orders
Species
The fundamental unit of taxonomy is the species. This is a group of very similar individuals that have the potential to interbreed freely, to produce fertile offspring - but cannot interbreed successfully with individuals from other species.
Hence, the mule is a cross between 2 species (the horse and the donkey) but is infertile - as is the zho, a cross between the Himalayan yak and a domestic cow (and with its 'alt. sp.' of "zo", a very useful word in Scrabble© it is too!).
(There are, as ever, exceptions where the rule breaks down, especially in the plant Kingdom. However, in the majority of cases, interbreeding of species does not produce fertile offspring.)

In palaeontology however, it can never be known for certain whether a population with a particular morphology was reproductively isolated or not. Hence, the definition of a fossil species (and most living specimens) must be based almost entirely on morphological criteria. Sometimes, this can be supplemented by a comparison of the chemistry of the shell, but only rarely.

The scientific name for a species consists of 2 parts - it is binomial, with a generic name followed by a trivial (or specific) name.
It is always given in italics, and both names begin with a capital letter, such as Echinocorys Scutata

A species may sometimes be further divided into sub-species, in which case it will have three names. [the third being its WHAT is is called?]

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Genus
The generic name refers to the genus, which is a group of species that are fairly closely related - such as the genus Equus which includes several species, such as the Equus caballus, Equus asinus and Equus zebra (domestic horse, wild ass and zebra respectively).
The generic name (Equus) can be used alone, to describe a genus, whereas the specific name is always used with the generic name - it is meaningless when used alone.

The generic name always begins with a capital letter, and generic and species names are always printed in italic (or underlined when writing or typing, when italic is not available).

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Family
Genera are grouped into families, which are major groups of generally similar organisms; such as Felidae, which includes all cat-like animals from domestic cat to wild lynx to tiger to cheetah to jaguar to snow leopard.
Every continent (with the exception of Australia and Antarctica) has its own genus of cat, but all are of the Felidae family.

Family names always end in the letters "ae", but are not printed in any special way.

Order
Families are grouped into orders, whose individuals may vary in many ways; such as the order of Carnivora - which includes cats, dogs and weasels.
However; all members vary significantly from the plant-eating animals, such as those in the major order Artiodactyla, which includes the pigs, deer, giraffe and antelopes.

Orders begin with a capital and usually end in "a" - but not always, so it is not always easy to tell what is an order!

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Class to Kingdom
Orders are grouped into classes, classes into phyla and phyla into kingdoms.

Class
The class is a major division within the animal Kingdom, and form the basis on which most fossil study is based.
For example, the phylum Molluscas contains 4 classes: the Gastropoda, Cephalopoda, Pelecypoda and Scaphopoda, of which Gastropoda and Cephalopoda are common vocabulary within the geological, and palaeontological worlds.

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Phylum
Classes are grouped into phyla (the plural of phylum), and phyla into Kingdoms.
There are only about 30 phyla in the animal kingdom, and only about a dozen of these (including Mollusca and Brachiopoda) leave any fossil remains. Thus, the vast majority of life has left no evidence for us to find.

Within the animal Kingdom, Animalia, the most common phyla are:

•Arthropoda (e.g. insects)
•Mollusca (e.g. snails)
•Chordata (e.g. fishes, amphibians, reptiles, birds, mammals)
•Platyhelminthes (e.g. tapeworms)
•Nematoda (i.e. unsegmented worms)
•Annelida (i.e. segmented worms)
•Cnidaria and Ctenophora (e.g. jellyfish)
•Echinodermata (e.g. starfish)
•Porifera (e.g. sponges - * see below)
The phylum Mollusca contains 4 classes: the Gastropoda, Cephalopods, Pelecypoda and Scaphopoda.

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Kingdom
Various web resources list either 3, 4 or 5 Kingdoms of life, the most common being that of:

Monera : prokaryotes (i.e., without a nucleus)
Protista : single-celled eukaryotes
Fungi : unique group of eukaryotes (based on nutrition)
Planta : multicellular algae and plants
Animala : multicellular animals

However; the current favoured hierarchy has a further highest level, that of the Domain, which contain 7 Kingdoms between them.

The domains and kingdoms recognised today are :

Domain Kingdom
Bacteria
(Eubacteria) bacteria
Archaea Crenarchaeota
Euryarchaeota
Eukarya Protoctista
Plantae
Fungi
Animalia
(sometimes 'Anamalia')

* The Kingdom Animalia is sometime termed the Metazoan. However the Metazoan is more accurately a SubKingdom of Animalia, as it excludes the Porifera (e.g. sponges)

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Defining the Hierarchy
As already described, allocations of individuals into each division is not an easy task, and the classifications can change. These changes occur at every level from domain or kingdom down to species.
In attempting to assign a fossil or an organism to a species, or a species to one of the higher divisions, there are a number of schemes used. No one is universally accepted method, and different taxonomists favour different approaches. In recent years, 3 sharply-contrasting schools have emerged, being:

•evolutionary taxonomy
•numerical taxonomy
•cladism
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Evolutionary Taxonomy
Until the 1970's, most palaeontologists - especially those working with fossil material collected from the field - were evolutionary taxonomists. In constructing an hierarchy, a traditional and very flexible combination of criteria was used.
Firstly, they used morphological resemblance - the extent to which the animals resembled each other.
Secondly, they used phylogenetic relationships - the way in which the animals actually related to each other, in terms of the recency of a common ancestor (as far as could be determined)

The order of succession in the rock record (biostratigraphy) and the geographical distribution, may play an important part in deciding these relationships.
This practical approach, which takes all factors into consideration, has long been the basis of palaeontological classification, and is still seen as the best method by many.

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Numerical Taxonomy
Major problems with the evolutionary method are seen because of the uncertainties and subjectivity of classification by observation, along with the limitations of the fossil record in terms of preservation.
To avoid this, numerical taxonomists attempt to use quantified observations of the animal in an attempt to decide on natural groupings. They consider that if enough characteristics are measured, quantified,and computed, then represented by the use of 'cluster scatters' (a form of graph) then the distance between clusters can be used as a measure of their differences.
However; although useful in some instances, the operator still needs to (subjectively) choose how best to analyse the measurements taken, and possibly give greater precedence (weight) to certain more-important characteristics - again, a subjective choice. Thus, numerical taxonomy is not as objective as it may first appear.

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Cladism
Cladism is a school of taxonomy founded in 1966. At its start it had both enthusiastic devotees and many doubters - but has now come to be recognised as the most effective method for reconstructing phylogeny. It relies upon phylogenetic criteria alone, by showing how features shared by organisms display a hierarchical pattern in nature. This is evident in the distribution of characteristics shared amongst organisms. Cladism assumes that the recency of common origin can best be shown by the shared possession of evolutionary novelties, or 'derived characters. Thus, in closely related groups we would see 'shared derived characters' which would distinguish that group from others.
The central concept of cladism is that any characteristic is either 'primitive' or 'derived'.
Thus; all vertebrates have backbones, so the possession of a backbone is primitive to all vertebrates and is not an indication of any relationship between any groups of, or individual, vertebrates.
A primitive characteristic of vertebrates is however, a derived characteristic compared to invertebrates. It is thus the sharing of both derived, and primitive, characteristics that establish the relative status of particular groups of characteristics within organisms.

A cladogram
The diagram shows a cladogram, which is a method to objectively determine the recency of common origin in related taxa, based upon primitive and derived characteristics.
Taxa A and B share a unique common ancestor, so are termed sister groups. They share an 'evolutionary novelty' not possessed by taxon C.
However; C is the sister group of the combination of taxa A and B, and similarly, D is the sister group of the combined taxa A, B and C.
In the construction of a cladistic analysis, a taxonomist assumes that dichotomous (2-way) branching has occurred in each lineage, and compiles an 'unweighted character data matrix'. Much data and computing power is used to build vast databases.

Three kinds of cladistic grouping have been distinguished:

•Monophyletic groups contain the common ancestor and all of its descendants: (D, C, B, A and X, Y, Z); or (A, B and X) in the diagram
•Paraphyletic groups, descended from a common ancestor (probably extinct, and known as a 'stem group' - A and B, but not the extinct X)
•Polyphyletic groups, the results of convergent evolution. Their representatives are descended from different ancestors so, although they may look similar, the 'grouping' is in fact artificial as far as a shared common ancestor with the shared characteristics is concerned.











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