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TAXONOMY - The science of naming things is called taxonomy.  

Taxonomy classification introduction and tutorial:

Excerpts highlighted in yellow from:  " Microsoft® Encarta® Online Encyclopedia 2000
http://encarta.msn.com © 1997-2000 Microsoft Corporation. All rights reserved.

Taxonomy, science of classifying organisms. Probably the first scientific study of plants was the attempt to classify them. At first, because of the limited knowledge of plant structures, artificial classifications, beginning with the most ancient one into herbs, shrubs, and trees, were necessary. These simple categories merely cataloged, in a tentative way, the rapidly accumulating material, in preparation for a classification based on natural relationships. Modern taxonomic classification, based on the natural concepts and system of the Swedish botanist Carolus Linnaeus, has progressed steadily since the 18th century, modified by advances in knowledge of morphology, evolution, and genetics. See Classification.
"Taxonomy," Microsoft® Encarta® Online Encyclopedia 2000
http://encarta.msn.com © 1997-2000 Microsoft Corporation. All rights reserved.

*(See note below) All living things are organized into a family tree starting with 5 "Kingdoms".  (Super kingdoms are - 1. Prokaryotae and 2. Eukaryotae.)

1. Bacteria (Monera)   2. Protista    3.  Fungi    4. Plants   5. Animals

Five Kingdoms


Cell type







Absorb, Photsyn., Chemosyn.

Bacteria, Cyanobacteria



Unicellular or colonial

Ingest, Photosyn.

Protozoa, Algae





Fungi, yeast, molds











The next level of the family tree under each of these kingdoms is called "Phyla". The plural of  phylum is phyla.   The animal (animalia) kingdom for example is divided into approximately 38 smaller phyla branches of the tree.  The next levels down the tree are "Class", Subclass", "Order", "Suborder", "Family", "Genus", and "Species".   

Lets see how this would look for the "Paramecium" which is a common pond microscopic animal. 

Kingdom  Animalia  (Protista - * see note below)
Class  Ciliatea
  Subclass  Rhabdophorina
Order  Hymenostomatida
  Suborder  Peniculina
Family  Parameciidae
  Genus  Paramecium
Species  aurelia, bursaria, or caudatum ..............

*NOTE:  The reference for this information is from Volume 1 of "Synopsis and Classification of Living Organisms" by Sybil P. Parker, ©1982, McGraw Hill. The following is extracted from that publication.  

"The classification used in these volumes recognized four kingdoms (Virus, Monera, Plantae, and Animalia) arranged in two superkingdoms - the Prokaryotae and the Eukaryotae.  Almost all workers agree that these two superkingdoms reflect a basic difference in organization of living organisms.  Decision on this arrangement is based on a compromise between the most useful groups and the highest degree of monophyly of these taxa.  The kingdoms recognized herein and some of the subkingdoms are still minimally mono phyletic.  Many workers will disagree with certain aspects of this classification, especially not recognizing the Protista.  Although this four-kingdom system advocated herein has the greatest advantage, the differences between it and some other systems, such as a five kingdom system recognizing Protistia, are not significant."

There are many species of the Genus Paramecium.  Three of them are Paramecium aurelia,  Paramecium bursaria, and the  Paramecium caudatum.  Notice that the first part of the name (Genus) is capitalized and the second (Species) name is not.  That is the standard way to write the names.  These names are similar to your name - they specify you in particular.  You wouldn't be expected to know the names of every person in your country so don't expect to memorize all the various species as there are millions of them.  Just concentrate on a few like you do your family and friends names.  

A great searchable database: ITIS Advanced Search (http://www.itis.usda.gov/advanced_search.html).

Another searchable taxonomy database:  Species 200) (Fish Database).

Taxonomy Database Search  http://www.ncbi.nlm.nih.gov/Taxonomy/

Dog Taxonomy: Canis familiaris

Other names:
synonym: Canis lupus familiaris
synonym: Canis domesticus
synonym: Canis canis
common name: dogs
includes: beagle dogs
includes: beagle dog


Taxonomy data and links http://www.geocities.com/RainForest/Vines/8695/data.html

Taxonomic Checklists

 Birds of the World on the Web
 Birds of the World Nomenclature Checklist
 Bird Families of the World
 Checklist of World Birds
 Clements' Checklist of Birds of the World
 Catalogue of South American Cichlidae
 Classes, Orders, and Families of Living Fishes
 Classification of Reptiles
 Complete List of Dinosaur Genera
 Dinosaur Classification
 Dinosaur Checklist
 Dinosaur Checklist of Families
 Diptera Family Name List by Groups
 Index Virum - Virus Names
 Insect Families and Subfamilies
 Insect Orders Checklist
 Invertebrates Checklist
 List of All Living Cephalopod Species
 A Checklist of the Mammals of the World
 Checklist of Mammal Families of the World
 Mammal Species of the World
 Nomenclatural Classification of Sharks and Rays of the World
 Palm Genera of the World
 Synopsis of Valid Genera and Species of Laniatores Worldwide
 Synopsis of World Taxa - A List of Phyla, Classes and Orders Arranged Phylogenetically
 Vascular Plant Families of the World

Taxonomy of all virus orders, families, genera and type species:


Taxonomy Detailed information and examples and links to database searches are found on our Microscopy Page Paragraph 3.

Classification online textbook

Taxonomy Browsing:


Kingdom Protista
101 Taxonomy - www.101science.com
Systematics of the Eukaryota

UCMP Web Lift to Taxa

Protista Taxonomy

Protista Taxonomy

Biology of Animals & Plants - Classifying Living Things

IWS Image Library Taxonomy

Lab 1: Taxonomy/Protista/Porifera

taxonomy notes bI

JSTOR: Evolutionary Relationships among Protozoa.

JSTOR: Some Paradoxes in Taxonomy with Reference to the Protista

Protist - Wikipedia, the free encyclopedia

Search results for research title

Kingdom Protista - Nomenclature & Taxonomy - The Taxonomicon

Biology 203 Lab

Amazon.com: Monerans & Protists (Taxonomy): Books: Dr.Alvin

Kingdom Protista

Introduction to the Protists

Diversity of Life Web Index

Taxonomy Software 

This is a list of some taxonomic and phylogenetic software, with emphasis on tree building and molecular data. There are also links to other, more extensive collections that may have what you're looking for if you can't find it here.

Phylum, in biology, major category, or taxon, of organisms with a common design or organization. This design is shared by all members of the phylum, even though structural details may differ greatly because of evolution. The assumption is made by biologists that all members of a phylum have a common ancestry.

A phylum is part of the hierarchy of classification of organisms. It is an arbitrary grouping; that is, it is developed from a combination of scientific observation, theorizing, and guesswork in an attempt to find order in the complexity of living and extinct life forms. The same is true of all classification levels above and below it except for species, which consist of organisms known to be capable, at least potentially, of interbreeding (see Species and Speciation).
"Phylum," Microsoft® Encarta® Online Encyclopedia 2000
http://encarta.msn.com © 1997-2000 Microsoft Corporation. All rights reserved.

Genus, in biology, category of classification of living things; specifically, a group of species (see Species and Speciation) closely related in structure and evolutionary origin. The position of a genus, in classification of the kingdoms of living forms, is below family or subfamily, and above species.

A genus name always differs from the name used for any other genus of living forms. An organism is named by assigning it a binomial, consisting of a genus name followed by a species name. In the scientific name of the tiger lily, Lilium tigrinum, for example, Lilium is the genus name and tigrinum is the species name. In zoological nomenclature, the genus and species names may be identical; the gorilla, for example, is Gorilla gorilla. In botanical nomenclature, the genus name may never be assigned as a species name. The scientific name applied to a family is always a modification of the name of one of the genera; the genus involved is termed the type genus.
"Genus," Microsoft® Encarta® Online Encyclopedia 2000
http://encarta.msn.com © 1997-2000 Microsoft Corporation. All rights reserved.


I. Introduction

Classification, in biology, identification, naming, and grouping of organisms into a formal system based on similarities such as internal and external anatomy, physiological functions, genetic makeup, or evolutionary history. With an estimated 10 million to 13 million species on Earth, the diversity of life is immense. Determining an underlying order in the complex web of life is a difficult undertaking that encompasses advanced scientific methods as well as fundamental philosophical issues about how to view the living world. Among the scientists who work on classification problems are systematists, biologists who study the diversity of organisms and their evolutionary relationship. In a related field known as taxonomy, scientists identify new organisms and determine how to place them into an existing classification scheme.

Classification determines methods for organizing the diversity of life on Earth. It is a dynamic process that reflects the very nature of organisms, which are subject to modification and change over many, many generations in the process of evolution. Since life first appeared on Earth 3.5 billion years ago, many new types of organisms have evolved. Many of these organisms have become extinct, while some have developed into the present fauna and flora of the world. Extinction and diversification continue nonstop, and scientists are frequently encountering fluctuations that may affect the way an organism is classified.

In addition to ordering organisms, scientists give a new species a scientific name, typically a two-word name in Latin, to distinguish it from similar organisms. This naming process creates a standard way for scientists around the world to communicate about the same organism. This standard minimizes confusion, particularly when common names are applied to organisms. For instance, the bird Europeans commonly call a robin is a different species of bird from the robin Americans recognize. The confusion ends when the birds are referred to by their scientific names: the European robin is Erithacus rubecula, while the American robin is Turdus migratorius.

When classifying organisms, scientists study a wide range of features, including those visible to the naked eye, those detectable only under a microscope, and those that can be determined only by chemical tests. Scientists compare the external shapes and sizes of organisms as well as the anatomy and function of internal organs and organ systems, such as the digestive or reproductive systems. Biochemists study and compare the molecular interactions within an organism that enable it to grow, make and store energy, and reproduce. The early stages of an organism's development, or embryology, as well as an organism's behavior, or ethology, are also useful in grouping organisms. Even the role an organism plays in its habitat can help place it in a particular group. Scientists use the fossil record to learn how certain animals have changed and evolved through Earth's history, which may provide clues for classification.

More recently, scientists have employed the techniques of molecular biology to compare the units of heredity, or genes, among organisms. Scientists study the fundamental units of deoxyribonucleic acid (DNA), the molecule that makes up genes, and organisms that share a similar DNA structure may be more closely related. Called molecular systematics, this approach is a powerful analytical tool. Used in combination with the other features studied in classification, molecular systematics can provide valuable insight into classification problems. For many organisms, molecular systematics studies have supported traditional classification; however, in some cases, the evidence from genetics studies has indicated that organisms should be reclassified. Skunks, for example, traditionally have been classified with badgers, ferrets, and minks in the family Mustelidae. But recent studies of molecular traits indicate that skunks differ significantly from these animals and may warrant classification in their own family.

II. How Species are Grouped

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Scientists classify organisms using a series of hierarchical categories called taxa (taxon, singular). This hierarchical system moves upward from a base containing a large number of organisms with very specific characteristics. This base taxon is part of a larger taxon, which in turn becomes part of an even larger taxon. Each successive taxon is distinguished by a broader set of characteristics.

The base level in the taxonomic hierarchy is the species. Broadly speaking, a species is a group of closely related organisms that are able to interbreed and produce fertile offspring . On the next tier of the hierarchy, similar species are grouped into a broader taxon called a genus (genera, plural). The remaining tiers within the hierarchy are formed by grouping genera into families, then families into orders, and orders into classes. In the classification of animals, bacteria, protists (unicellular organisms, such as amoebas, with characteristics of both plants and animals), and fungi, classes are grouped into phyla (see Phylum), while plant classes are grouped into divisions. Both phyla and divisions are grouped into kingdoms. Some scientists go on to group kingdoms into domains.

III. Classification Methods

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Grouping organisms according to shared characteristics is not a simple task, and scientists often disagree about the best way to classify organisms. Some think that organisms should be grouped according to differences or similarities in the way they look or act. Other scientists argue that classification should be based on characteristics derived from a shared evolution. Conflicting philosophies about classification have resulted in a variety of classification methods, each with their own set of assumptions, techniques, and results.

The classification of insects, birds, and bats illustrates a traditional classification process. Insects, birds, and bats are all animals—that is, they are multicellular organisms that obtain energy from food. Scientists group these organisms into the Kingdom Animalia.

Birds and bats both have spinal cords, causing scientists to classify both birds and bats in the phylum Chordata. Within the phylum Chordata, key features cause scientists to separate birds and bats. Birds are placed in the class Aves, which includes egg-laying animals, while bats are placed in the class Mammalia, which includes animals that give birth to live young and nurse their young from mammary glands. Insects, which lack spinal cords, are classified in the phylum Arthropoda, the taxon that includes animals with jointed legs and a skeleton on the outside of the body. Insects are further divided based on such broad physical features as the presence or absence of wings.

Scientists using the classical approach must judge the relative importance of characteristics. They may decide, for example, that wing structure is more important than the presence of fingernails in certain cases of classification. Some critics argue that this interpretation and evaluation is too subjective. To introduce more objectivity into classification, some scientists devised the phenetics approach to classification.

In the phenetics approach, scientists rely on quantitative methods and consider only the observable characteristics of modern organisms. Pheneticists identify a set of characteristics to measure and assign a certain numerical value to each characteristic. The tally is used to determine the extent of similarity between organisms. For example, pheneticists may find that, overall, birds and reptiles have a 77 percent similarity of body structure, or morphology, compared to a 55 percent morphological similarity between birds and mammals. From this measurement, pheneticists would suggest a classification that grouped birds and reptiles more closely than birds and mammals.

A third classification method is the cladistic approach, which strives to classify organisms by natural evolutionary relationships, known as phylogeny. Cladists use the fossil record, molecular genetics, and other techniques to create an evolutionary tree called a cladogram. This branched diagram shows the relationship of a group of species based on the fewest number of shared changes that have occurred from generation to generation.

IV. History of Classification Systems

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Classification is one of the oldest sciences, but despite its age it is still a vigorous field full of new discoveries and methods. Much like other fields of science, great thinkers have shaped the course of classification. One of the earliest classification schemes was established by Greek philosopher Aristotle, who lived in the 300s BC. Aristotle believed that the complexity of life could be divided into a natural order based on dichotomies, or polar opposites. For example, Aristotle divided animals into those with blood and those without blood, a classification that roughly corresponds to the division between vertebrates and invertebrates used in contemporary classification schemes.

Aristotle wrote extensively on both plants and animals, but his writings on plants were lost. Fortunately, his pupil Theophrastus applied Aristotle's taxonomic approach to the study of plants in his work Inquiry into Plants (trans. 1916). Theophrastus subdivided plants, based on shape, into such broad categories as trees, shrubs, and herbs. A more pragmatic approach to classification was developed by Greek physician Dioscorides, who separated, for instance, medicinal herbs from those used in making perfumes.

To unify the naming of organisms and to communicate more precisely about the increasing number of species being discovered, scholars in the Middle Ages (around the 5th century to the 15th century AD) translated the common names of organisms into Latin—at the time the language of educated persons. These names were often long and cumbersome, and included numerous descriptive terms. This complex naming process was simplified into a two word, or binomial, naming system in the mid-16th century to mid-17th century by a group of naturalists known as herbalists.

Sixteenth-century Italian botanist Andrea Cesalpino was the first scientist to classify plants primarily according to structural characteristics, such as their fruits and seeds. Cesalpino developed a method of character weighting in which he defined certain key characteristics that were important for recognizing plant groups. This method was adapted by Swiss botanist Caspar Bauhin, who catalogued an extensive list of plants. More importantly, Bauhin was the first to organize plants into a crude system that resembles modern genera and species.

Animal classification also advanced in the 16th century. French naturalist Pierre Belon extensively studied and catalogued birds. He was the first to use adaptation to habitat to divide birds into such groups as aquatic birds, wading birds, birds of prey, perching birds, and land birds, categories still used informally today. In the 17th century, English naturalist John Ray was the first to apply the character weighting method to structural features in animals. He used key characteristics, such as the shape and size of the bird beak, to classify birds.

In the mid-1700s, Swedish naturalist Carolus Linnaeus established clear rules for a two-name system called the binomial system of nomenclature. In this system, similar organisms are grouped into a genus, and each organism is given a two-word Latin name. The first word is the genus name, and the second word is usually an adjective describing the organism, its geographic location, or the person who discovered it. Using this system, the domestic dog is Canis familiaris. Canis is the genus name for the group of animals that includes dogs, wolves, coyotes, and jackals. The word familiaris acts as a descriptor to further differentiate the domestic dog from its wild cousins.

Prior to Linnaeus, biologists had established random categories of classification, such as the category of genus for a group of species. Linnaeus was the first to formalize the use of higher taxa in his book Systema Naturae (1735), establishing the standard hierarchy taxonomy still in use today. In addition, Linnaeus devised logical rules to classify species that continued to be used by scientists for over 200 years.

Before the 19th century, Linnaeus and other taxonomists classified organisms in an arbitrary but logical way that made it easier to communicate scientific information. But with the publication of On the Origin of Species in 1859 by British naturalist Charles Darwin, the purpose of classification took on new meaning. Darwin argued that classification systems should reflect the history of life—that is, species should be related based on their shared ancestry. He defined species as groups that have diverged from a shared ancestry in recent history, while organisms in higher taxa, such as genera, class, or order, diverged from a shared ancestor further back in history. Making evolutionary history compatible with the classification systems already established was no easy task, however. Critics argued that classification should be consistent with phylogeny, but not based solely upon evolutionary history. They advocated using other factors, such as behavior or anatomy, along with phylogeny to better classify organisms. This controversy over the fundamental approach to classification continues today.

The development and use of microscopes in the late 16th century revealed a diverse array of single-celled organisms. These organisms presented new classification problems for the science community, which still relied on a two-kingdom classification system. At first, single-celled organisms that carried out photosynthesis were classified in Kingdom Plantae, and organisms that ingested food were placed in Kingdom Animalia. By the 19th century, scientists had identified a wide variety of microscopic organisms with diverse cell anatomies, specialized internal structures called organelles, and reproductive patterns that did not easily fit into the plant or animal classification system. This great diversity prompted German biologist Ernst Haeckel to propose placing these unicellular forms in a third kingdom, th

Haeckel placed bacteria within the Kingdom Protista in a separate group that he called Monera, recognizing that these organisms differed from all other cells because they lacked nuclei. As biologists learned more about bacteria, they became aware of the further differences between these organisms and all other life forms. In addition to lacking nuclei, bacteria differ from other types of cells in that they do not have membrane-bound organelles, such as mitochondria, the cell structures involved in energy metabolism. In the 1930s, these differences led French marine biologist Edouard Chatton to make a crucial distinction between prokaryotes, organisms such as bacteria that lack nuclei, and eukaryotes, more complex organisms that have nuclei. In 1938 American biologist Herbert Copeland argued that the distinctions between prokaryotes and eukaryotes were so fundamental that prokaryotes merited a fourth kingdom of their own called Kingdom Monera (now called Kingdom Prokaryotae).

In the 1950s, American biologist Robert H. Whittaker proposed adding a fifth kingdom, Kingdom Fungi, based on fungi's unique method of obtaining food. Fungi had previously been classified with plants, but Whittaker argued that fungi do not make their own food, as plants do, and they do not ingest it, as animals do. Rather, fungi secrete digestive enzymes around their food, breaking it down before absorbing it into their cells.

By the 1970s, advances in molecular systematics provided new insights about relationships among organisms and revealed imperfections in the current classification systems. New molecular biology techniques, such as polymerase chain reaction, which permits the easy analysis and comparison of DNA structures, enabled American microbiologist Carl Woese to determine that a group of organisms formerly classified as bacteria actually belong to a separate taxon. Archaea, also known as archaebacteria, were found to have unique molecular structures and physiological characteristics. Archaea are represented by a relatively small group of single-celled organisms that mostly live in extremely hot, salty, or acidic anaerobic environments. Woese initially proposed a six-kingdom classification system, in which he separated prokaryotic organisms into two kingdoms, the Archaebacteria and Eubacteria, or true bacteria, and placing eukaryotic organisms into the Kingdoms Plantae, Animalia, Fungi, and Protista. He later advocated the use of a new category called the domain. In his new system, all life forms are grouped into three domains: bacteria, archaea, and eukarya.

Other scientists propose an eight-kingdom system. In addition to the Plantae, Animalia, and Protista kingdoms, this system also includes two prokaryote kingdoms of Archaea and Eubacteria, and divides Kingdom Protista into three separate kingdoms.

No matter what method is used to classify an organism, its place in the hierarchy of life is not fixed. Scientists continue to uncover new evidence from the fossil record, molecular biology, or other fields that may change an organism's place in the classification hierarchy.

See an outline for this article.

"Classification," Microsoft® Encarta® Online Encyclopedia 2000
http://encarta.msn.com © 1997-2000 Microsoft Corporation. All rights reserved.

Other web links you may find useful.

Curiosities of Biological Nomenclature Mark Isaak

Taxonomy  http://www.geocities.com/RainForest/Canopy/3220/taxonomy.html

Plant Taxonomy Database GRIN  http://www.ars-grin.gov/npgs/tax/

Flowering Plant Taxonomy  http://www.colby.edu/info.tech/BI211/

Zoological (zoology) Record  http://www.york.biosis.org/zrdocs/zoolinfo/syst_tax.htm

Kingdoms Project   http://www.il-st-acad-sci.org///kingdoms.html

Keys to Soil Taxonomy  http://www.statlab.iastate.edu/soils/keytax/

Ideas in Bloom : Taxonomy-Based Activities for U.S. Studies

Classification Online Textbook - All you need to know about classification.

Taxonomy Table  http://library.thinkquest.org/11771/english/hi/biology/taxonomy.shtml

Taxonomy - Microscopic  http://medic.med.uth.tmc.edu/path/00001458.htm

Curiosities of Biological Taxonomy 
Major Categories in the Taxonomy of Educational Objectives 
Taxonomy Lab: An exercise in taxonomy, evolution, and classification, Interdisciplinary
Learning Skills Program - Bloom's Taxonomy 
Taxonomy and Systematics at Glasgow 
Taxonomy Browser

Tree of Life

Entrez Taxonomy


Learning Skills Program - Bloom's Taxonomy

Major Categories in the Taxonomy of Educational Objectives


Taxonomy - Wikipedia, the free encyclopedia

Learning Skills Program - Bloom's Taxonomy

NCBI Taxonomy Homepage

Taxonomy on the Web

Taxonomy Warehouse - A Comprehensive Web-Directory of Taxonomies

Bloom's Taxonomy

Major Categories in the Taxonomy of Educational Objectives

Supernova Taxonomy

Taxonomy Lab: An exercise in taxonomy, evolution, and 


Educational Psychology Interactive: The Cognitive Domain

A Taxonomy of WebQuest Tasks

Bloom's Taxonomy

UCMP Web Lift to Taxa


Critical Thinking Across the Curriculum Home Page


CSIRO PUBLISHING - Invertebrate Systematics

Soil Taxonomy | NRCS Soils

Lexonomy | A Taxonomy Primer

UCMP Web Lift to Taxa
www.ucmp.berkeley.edu/help/taxaform.html - 2k - Cached - Similar pages

Taxonomy Lab: An exercise in taxonomy, evolution, and ...

Bloom's Taxonomy


TAXONOMY  Excellent material here!


Taxonomy Detailed information and examples and links to database searches are found on our Microscopy Page Paragraph 3.

Classification online textbook

Evolution web sites:

For information on the Cambrian period: 
For information on the "tree of life" (quite relevant to taxonomy): 
For general information on evolution: 

Evolution is based on scientific evidence.  

See additional information on our "Microscope" page.

For lot's of paramecium links go to "101 Microscopy  Page Two", or to "Paramecium".

Taxonomy for Learning, Teaching, and Assessing, A: A Revision of Bloom's Taxonomy of Educational Objectives
Introduction to the Principles of Plant Taxonomy

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