1. CLASSIFICATION OF ORGANISMS chapter 15
BENEDY SOKI SIHERYA
S215A002

2. introduction
Diversity of life is highly observed among members of the species and much more between species. About 1.5 million different species of animals, plants and other organisms have been identified, described and named, with about 10 to 100 million different existing species which are yet to be identified. It is extensive work to manage this diversity presented in such a large number.
Therefore, one of the major goals in biology is to identify, characterize and classify organisms. This is important because it is easier to study, gather and communicate information about the features of organisms when they are organized in groups.
The principal tool for organizing organisms is called biological classification.
Biological classification is the grouping of organisms into specific categories based on a set of criteria. In this chapter, we will study about the categories of organisms in current biological classification and the basic common classification systems.

3. 15.1 CLASSIFICATION SYSTEMS
Taxonomy is a branch of systems biology that involves identification, describing, naming and classification of organisms based on the natural relations of all other organisms.
Systems biology involves study and modelling of biological components including molecules, cells, organisms or entire species
Since several thousand years ago, a number of classification systems have been developed, and biological classification is not rigid. A classification system may be artificial or natural.

4. Artificial System of Classification
There are several possible ways of grouping organisms.
For instance, you could put all land animals in one group; all aquatic organism in another, or all green creatures in the same group. However, these do not make meaningful groups.
For example, sea weed and sharks are both aquatic organisms; plants and some snakes are green, but neither of these pairs has much in common. These would be artificial systems of classification.
The first widely accepted system was developed by a Greek philosopher Aristotle (394 BC – 322 BC) who classified organisms as either plant or animals. Also, animals where classified according to the presence or absence of blood. This system persisted for centuries but was artificial and had many limitations. It was based in the idea that all organism are unchanging, distinct and separate.

5. Natural System of Classification
The natural system of classification is the most useful system to biologists because it takes into account certain relationships among all organisms,
important features shared by as large group as possible, and puts related organisms into distinct groups.
It is scientific. The Linnaean system of classification is the most widely accepted natural system of classification used by biologists. This system, as the name points, was born of a Swedish botanists Carolus Linnaeus (1707 – 1778).
Linnaeus broadened the artificial classification systems that existed before and formalized them into one scientific system. He is also called the father of taxonomy because it is the Linnaean system of classification that became the first formal system of taxonomical organization and natural classification. Linnaeus, like others, based his system on studies of morphology and behavior of organisms on classification.

6. 15.2 NAMING ORGANISMS
Organisms are known by different common names in different locations of the world.
However, each organism has only one correct scientific name which anyone anywhere in the world can recognize.
The use of scientific names in Latin language avoids ambiguity and confusion that can be created with native name.
The scientific method of naming organisms, first introduced in 1753 by Carolus Linnaeus, is called binomial system of nomenclature or simply binomial nomenclature

7. Binomial nomenclature
Binomial nomenclature is a formal system of naming species in which each organism’s name has two parts.
The first part of the name is a genus (generic, plural) name to which a species belongs and the second part is the specific epithet or species name which indicates or identifies a particular species.
Binomial nomenclature is based in Latin because Latin has been an unchanging language and has been a language of medicine, science and education in history.

8. writing scientific names
In classification, the following guidelines are used when writing scientific names using binomial nomenclature:
The first letter of the genus name is always capitalized, but the rest of the letters of the genus name and all the letters of the species name (epithet) are lowercase.
When written in printed on paper, book, magazine or any printed form, the scientific name should be italicized.
When written by hand, both parts of the scientific name should be underlined.
When abbreviating the scientific name, often in latter appearances in passages or chapter, after if it had been written completely before, the genus name is abbreviated to the first letter. E.g. Homo sapiens can be abbreviated as H. sapiens.

9. 15.3 TAXONOMY AND CLASSIFICATION
A taxon (taxa, plural) is a named group or level of organisms. Taxa at the top of the hierarchy have much more and broader characteristics while those the bottom have specific characteristics.
in the hierarchy in order of descent include Domain, Supergroup*, Kingdom, Phylum or Division, Class, Order, Family, Genus and Species.
The broadest of all taxa is the domain. Domain comprises supergroup taxa. A taxon composed of related phyla is kingdom. A phylum or division is a group of similar classes, a class of related orders, an order of related families, a family of apparently related genera a genus of similar closely related species, and a species of organisms that can interbred among themselves to produce fertile offspring. These taxa can be expanded as necessary to include clades, subgroups, superphyla, subphyla, superclasses, subclasses, infraorder, subspecies, etc., between these major categories.

10. 15.4 CLASSIFYING ORGANISMS
Organisms are classified differently at different levels.
Major features used in classification generally include cell types and structures, nutrition modes, number and composition of cells, genomic features, biochemical features and body symmetry and construction, especially for most multicellular organisms. Classification now relies heavily on phylogeny (comparison of genomic features).

11. domain, Supergroup and Kingdom
Known species were once classified only into two kingdoms: plants and animals. In the 1960’s five kingdoms were identified based on types of cells.
These included Monera (prokaryotes), Protista, Plantae, Fungi and Animalia.
It was later recognized that some prokaryotes were different from each other and biochemical studies showed that the unicellular archaea were significantly different from the rest of other unicellular bacteria.
Thus, kingdom Monera was split into bacteria and archaea.
Refined methods in classification led to the development of the three-domain, six kingdom classification system. This system was developed from the previous classification system that did not contain domains and had five kingdoms as the highest taxa.
The domain which was proposed in the early 1990s, is currently the broadest taxa containing one or more supergroups or kingdoms. The three domains included Bacteria, Archaea and Eukarya and the six kingdoms were Bacteria, Archaea, Protista, Fungi, Plantae and Animalia.

12. Continued……..
Since 2000, classification of eukaryotes has drastically changed. Now, kingdom Protista has become obsolete as was Monera.
This is because it includes some members that are more closely related to animals, plants or fungi than they are to other protists based on genetic sequencing.
A super group taxa was introduced in the hierarchy of classification in 2005 after the crumbling of kingdom Protista.
The new system of classification revised in 2012 now recognizes three domains (Bacteria, Archaea and Eukarya) with domain Eukarya consisting of seven super groups (Unikonta, Archaeplastida, Excavata, Rhizaria, Alveolata, Stramenopiles and Hacrobia).

13. Domain Archaea
Archaea are prokaryotic organism which are members of the domain and kingdom archaea. They are unicellular organisms with cells walls not made of peptidoglycans.
They are extremophiles because they live under extreme conditions of high temperature and salinity.
They are found in boiling hot springs, thermal vents on oceans floors, in the mud of marshes and in salty water bodies such as lakes.
Domain Eukarya Eukaryotes are organisms with cells that have a true nuclei and membrane-bound organelles, and are members of domain Eukarya.

14. super groups This domain consists of the following super groups:
Unikonta (Amorphea) which includes kingdom Animlia and Fungi,
Archaeplastida, which includes kingdom Plantae,
Excavata,
Rhizaria,
Alveolata,
Stramenopiles and
Hacrobia

15. Kingdom Animalia
Kingdom Animalia consists of eukaryotic organism that are multicellular, whose cells lack cell walls and chloroplasts (plastids).
Members of this kingdom Animalia are called animals, and animals are generally motile. They are all heterotrophic (do not make their own food).
They live in water, on land and in the air. Most animals are organized into complex tissues, organs and systems.

16. Kingdom Fungi And Protists
Kingdom Fungi consists of eukaryotic organisms that are either unicellular or multicellular. Members of the Kingdom Fungi are called fungi (fungus, singular).
Fungi obtain food nutrients from organic materials from the environment by absorption. They are heterotrophic, do not move, lack organs, have cells with cell walls made of chitin and most are made of threadlike structures called hyphae
Protists include informal category of diverse eukaryotic organisms which are either unicellular, colonial (exist in colonies) or multicellular and are neither animals, plants nor fungi.

17. Continued…….
Protists, lack organs and are extremely diverse from each but do not fit also into other kingdoms.
These organisms, once placed in kingdom Protista or Protoctista, have now been disseminated and placed into different supergroups and clades together with animals, plants and fungi based on phylogenetics.
The three broad categories of protists, based on nutrition, includes plant-like protists called algae, animal- like protists called protozoans and fungus-like protists called slime molds or meldews.
Some protists such as euglenoids have both plant-like and animal-like features but predominantly plant- like because they can photosynthesize.
Because of some ambiguity in current characterization in domain Eukarya, especially related to protists’ classification, we will discuss diversity of protists based on nutrition.

18. METHODS AND FEATURES USED IN CLASSIFICATION OF ORGANISMS
Keys for Identification:
Dichotomous Keys
When the main features or characteristics of a group of organisms are known and described, a systematic key plan can then be designed to be used for identifying and categorizing a new unknown or unfamiliar organism.
Biologists have drawn such keys for grouping organisms.
Dichotomous keys are one of such tools. A dichotomous key is a form of an identification key that consists of a series of choices that lead the user to the correct identification of an organism.
It compares the features of an unknown organism with the features of known organisms and uses a series of ‘yes’ or ‘no’ questions allowing you to choose only one feature.
Dichotomous means ‘two branches’. So you can only be faced with two possibilities at each stage from which you have to choose.

19. Characteristics Used in Classification To identify and classify a species using keys and other identification procedures, characters, which are variable inherited features among organism, are used.
Major characters usually includes the following:
Morphological features involving comparisons of appearances of organisms.
Biochemical and Physiological features involving comparisons of chemistry of biological molecules such as amino acids and nucleotides and how organisms function chemically at different levels on their bodies.
Genomic features involving comparisons from DNA, RNA and protein analysis, comparisons of chromosome number and structure and comparisons of genomic sequences between organisms.

20. Determining Species
As you might expect, the classification of organisms is intricate at species taxa than at any other level in the hierarchy because of the similarities that might exists among organisms.
It is not always easy to define and describe a species. Several ways of determining and classifying a species exists. These include:

21. Morphological Topological Species Concept
This concept determines and classifies species based on comparisons of physical characteristics or traits with the type sample or specimen. One limitation to this concept of species classification is that different alleles of the same gene ma produce different traits within a species. Also, observing only physical traits may be subjective

22. Ecological Species Concept
This concept determines and classifies species based on its role in nature and its adaptation to specific functions in a community.
However, two organisms may be of one species but different in the way the feed, live and function in the community.
This could be a limitation to classifying organisms like such based on this concept.

23. Phylogenetic Species Concept
This concept determines and classifies species based on phylogeny – evolutionary history of organism.
It defines species as a group of individuals from a single ancestral parent.
It works well because it can account for extinct species but its limitation is that the history of species may not be known.

24. Biological Species Concept
This concept determines and classifies species as a group of organisms that are able to interbreed and produce fertile offspring in a natural environment.
It is the most commonly used method in classification.
One of the major limitations to the biological concept of species is that some different organisms, though considered not to be of the same species, can actually interbreed and produce fertile offspring.
For example, domestic dogs and wolves are classified as different species but they can interbreed and produce fertile offspring.
Also, another limitation is that extinct species cannot be classified based on this concept.

25. THE END