Systematics Based on Evolutionary Relationship

Systematics is the study of the kinds and diversity of organisms and of any and all relationships among them. Tracing
phylogeny is one of the goals of systematics; hence, it is considered as the study of biological diversity in an evolutionary
context. Systematists use data ranging from fossils to molecules and genes to infer evolutionary relationships. These
information enable biologists to construct a comprehensive tree of life that will continue to be refined as additional data
are collected.
Phylogeny-the evolutionary history of a species or group of species
Systematics- the study of the kinds and diversity of organisms and of any and all relationships among them.
Homology-similarity due to shared ancestry
Molecular clock- a yardstick for measuring the absolute time of evolutionary change based on the observation that
some genes and other regions of genomes appear to evolve at constant rates

Phylogenetic Trees
In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called its phylogeny.
A phylogeny describes the relationships of an organism, such as from which organisms it is thought to have evolved, to
which species it is most closely related, and so forth. Phylogenetic relationships provide information on shared ancestry
but not necessarily on how organisms are similar or different.

Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms.
A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms.
Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm
the proposed relationships.
A phylogenetic tree can be read like a map of evolutionary history.
Many phylogenetic trees have a single lineage at the base
representing a common ancestor. Scientists call such
trees rooted, which means there is a single ancestral lineage
(typically drawn from the bottom or left) to which all organisms
represented in the diagram relate. Notice in the rooted
phylogenetic tree that the three domains— Bacteria, Archaea, and
Eukarya—diverge from a single point and branch off. The small branch
that plants and animals (including humans) occupy in this diagram shows
how recent and miniscule these groups are compared with other
organisms. Unrooted trees don’t show a common ancestor but do show
relationships among species.

The point where a split occurs, called a branch point, represents where a single lineage evolved into a distinct new one.
A lineage that evolved early from the root and remains unbranched is called basal taxon. When two lineages stem from
the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves
to illustrate where scientists have not definitively determined all of the relationships. It is important to note that
although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved
from each other. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the
other.

Basic Taxonomic Concepts

DEFINATION:

Classification – method of grouping organisms; arranging entities into some type of order to provide a system for
cataloguing and expressing relationships between these entities
 - The arrangement of organisms into orderly groups based on their similarities. Also known as Taxonomy.

Benefits of Classifying - Accurately and uniformly names organisms, prevents misnomers such as starfish and jellyfish
that aren't really fish and use the same language, Latin or some Greek

Hierarchy- a system of organizing groups into ranks according to status; putting groups at various levels according to
importance or power
Nomenclature- the formal naming of taxa according to some standardized system. For plants, fungi, and algae, rules for
naming are provided by the International Code of Botanical Nomenclature. For animals, rules on naming are based on
the International Code of Zoological Nomenclature.
Identification- is the process of associating an unknown taxon with a known one
Description- is the assignment of features or attributes (characters) to a taxon
Taxonomy- the theory and practice of classifying organisms

Reminder:
Taxonomy is a major part of systematics that includes description, identification, nomenclature and classification

Taxonomists - Scientists that identify and name organisms.

*The word ‘taxonomy’ is derived from the Greek words taxis (=arrangement) and nomos (=law)

Early Taxonomists
Aristotle - First taxonomist, divided organisms into plants and animals and subdivided them by their habitat--land, sea
or air dwellers.
John Ray - Botanist was the first to use Latin for naming, very long descriptions telling everything about the plant
Carolus Linnaeus - 18th century taxonomist, "Father of Taxonomy" that classified organisms by their structure and
developed a naming system called Binomial Nomenclature. Genus and Species

Principles of Taxonomy

 Classification systems are used to name organisms and group them in a logical manner
 Taxonomy is the study of classification of living things
 Organisms are living things that can be assigned a classification based on their physical characteristics

Taxonomy is the part of science that focuses on naming and classifying or grouping organisms. A Swedish
naturalist named Carolus Linnaeus is considered the 'Father of Taxonomy' because, in the 1700s, he developed a
way to name and organize species that we still use today. His two most important contributions to taxonomy were:

1. A hierarchical classification system

2. The system of binomial nomenclature (a 2-part naming method)

During his lifetime, Linnaeus collected around 40,000 specimens of plants, animals, and shells. He believed it was
important to have a standard way of grouping and naming species. So in 1735, he published his first edition
of Systema Naturae (The System of Nature), which was a small pamphlet explaining his new system of the
classification of nature.
He continued to publish more editions of Systema Naturae that included more named species. In total, Linnaeus
named 4,400 animal species and 7,700 plant species using his binomial nomenclature system. The tenth edition
of Systema Naturae was published in 1758 and is considered the most important edition. Its full title in English
is System of nature through the three kingdoms of nature, according to classes, orders, genera and species, with
characters, differences, synonyms, places.
Linnaeus's Classification System
In Systema Naturae, Linnaeus classified nature into a hierarchy. He proposed that there were three broad groups,
called kingdoms, into which the whole of nature could fit. These kingdoms were animals, plants, and minerals. He
divided each of these kingdoms into classes. Classes were divided into orders. These were further divided
into genera (genus is singular) and then species. We still use this system today, but we have made some changes.
Today, we only use this system to classify living things. (Linnaeus included nonliving things in his mineral kingdom.)
Also, we have added a few additional levels in the hierarchy. The broadest level of life is now a domain. All living
things fit into only three domains: Archaea, Bacteria, and Eukarya. Within each of these domains there are
kingdoms.
For example, Eukarya includes the kingdoms Animalia, Fungi, Plantae, and more. Each kingdom
contains phyla (singular is phylum), followed by class, order, family, genus, and species. Each level of
classification is also called a taxon (plural is taxa).

(Note that it is standard practice to italicize the genus and species names).

What are the rankings in biological classification or 7 levels of classification?

The group kingdom, includes all living organisms and species. Phylum puts organisms that have a backbone, or no
backbone in to their own two groups. The classification group, class, divides organisms into groups like reptiles and
mammals. Order puts them in a general group of what they are, like the group turtle, which including all turtles.
Which group includes the most Species?
The Kingdom has the most Species, it has more than 270,000 Species. Species are put in this grouped by their basic
common characteristics.
Which group is the most specific?
The group that is most specific is species. Species is the smallest group of the seven classification levels. A species are
the organisms capable of producing fertile offspring. This will usually be true, but more precise measures are often used,
like DNA and the forming of living
organisms.

*The word ‘species’ is both in singular and

plural form; there is no such word as

‘specie’

*Classification is based on key characters/

features used in groupings. Take for
example the classification of humans. Refer
to the table below.

Dichotomous Keys

A dichotomous key is a tool that allows the user to determine the identity of items in the natural
world, such as trees, wildflowers, mammals, reptiles, rocks, and fish. Keys consist of a series of
choices that lead the user to the correct name of a given item. "Dichotomous" means "divided into
two parts". Therefore, dichotomous keys always give two choices in each step.
Aristotle was one of the first scientist to organize living things. Aristotle developed the first
classification system, which divided all known organisms into two

Aristotle was one of the first scientist to organize living things. Aristotle developed the first classification
system, which divided all known organisms into two groups:PLANTS and ANIMALS.

Aristotle then divided each of these main groups into three smaller groups.

Animal Subgroups: Land, Water, Air

Plant Subgroups: Small, Medium, Large

1. Animal with a shell Go to 2

Animal without a shell Go to 3
2. Shell is a flat coil Planorbis corneus, great ramshorn snail
Shell is a spiral Lymnaea peregra, wandering snail
3. Body is segmental Go to 4
Body is not segmental Polycelis felina, flatworm
4. No legs Go to 8
Jointed legs Go to 5
5. Three pairs of legs Go to 6
More than three pairs of legs Go to 7
6. Body flattened sideways Gammarus pulex, freshwater shrimp
Body flattened downwards, looks like a woodlouse Asellus aquaticus, water hog house
7. Two hooks on last segments Rhyacophila sp., caseless caddis fly nymp
Three tail appendages Baetis rhodani, mayfly nymph
8. Long breathing rube at end of body Eristalis sp., rat-tailed maggot
No long breathing tube Go to 9
9. Thin body, no suckers Oligochaete worm
Suckers at both ends Leech
Aristotle’s classification system was not very good. There were too many organisms that didn’t fit. For example, frogs
are born in water and have gills like fish, but when they grow up they have lungs and can live on land. So how would
Aristotle classify frogs? In Aristotle’s classification system, birds, bats, and flying insects were grouped together even
though they have little in common except they can fly. But the penguin is a bird that cannot fly. So Aristotle would not
have classified them as birds.

Even with the many problems of Aristotle’s limited classification system, it was used for nearly 2000 years until it was
replaced in the 1700s by the Swedish biologist, Carolus Linnaeus (1707-1778).

Linnaeus, like Aristotle, classified organisms according to their traits. The classification systems of both Aristotle and
Linnaeus started with the same two groups: Plants and Animals. Linnaeus called these groups, kingdoms. But, unlike
Aristotle, Linnaeus divided kingdom into five levels: class, order, genus, species, and variety. Organisms were placed in
these levels based on traits, including similarities of body parts , physical form such as size, shape, and methods of
getting food.

Linnaeus is known as the father of taxonomy. In addition to his expanding the classification system, he established a
simple way of naming each species. This is called a binomial naming system and it has two parts. The first part of the
species name identifies the genus to which the species belongs; the second part identifies the species within the genus.

For example, humans belong to the genus Homo and within this genus to the species sapiens, thus the two-part species
name for humans is Homo sapiens. The genus name is capitalized and each name is written in italics.

Glossary of terms related to classification and naming of organisms:

Classification – a system of naming objects or entities by common characteristics. In a biological sense, classification is
the systematic grouping of organisms based on structural or functional similarities or evolutionary history. A process of
establishing, defining, and ranking taxa within hierarchical series of groups.
Taxonomy – the classification of organisms into a system that indicates natural relationships (evolutionary
relationships); the theory and practice of describing, naming, and classifying organisms.
Systematics – the systematic classification of organisms and the evolutionary relationships among them; taxonomy.
Phylogeny – the evolutionary history of a group or lineage.
Nomenclature – the system of scientific names applied to taxa (groups of organisms).

Biological Nomenclature
One of the primary responsibilities of systematic biology is the development of our biological nomenclature and
classifications. Nomenclature is not an end to systematics and taxonomy but is a necessity in organizing information about
biodiversity. Nomenclature functions to provide labels (names) for all taxa at all levels in the hierarchy of life.

Biological nomenclature is, to some degree, the parlance of systematic biology. It derives from
the binomial (or binominal) nomenclature that was originally codified in the works of
Linnaeus, Species Plantarum (1753) and Systema Naturae, 10th Edition (1758). These
publications are the decided starting points for the modern biological nomenclature in most
groups of plants and animals.

Together with the presentation of the consistent binomial system of naming, Linnaeus also developed a system of
organizing the diversity of life in a hierarchical classification. Latin was the important language of the time of Linnaeus
and continues to be a critical language for international communication. As will be seen below the various Codes for
nomenclature consider Latin to be an essential language.

 Taxa at the level of species are named with binomials, consisting of generic and specific epithets or names that
together equal the species name
 Taxa above the level of species are Supraspecific Taxa and are Uninominals.
 Taxa below the level of species are Subspecies are are Trinominals.

The binomial system has been a successful system because it is functional, has been the only system that has been
universally accepted, and has been used over the last 250 of nomenclature. Recent literature, however, has examined some
alternative methods; these will not be covered herein.

Biological nomenclature is a language that we use to communicate ideas and information about the diversity of life. It is
an information retrieval system conveying information about diversity and relationships.

Binomial nomenclature ("two-term naming system") also called binominal nomenclature ("two-name
naming system") or binary nomenclature, is a formal system of naming species of living things by giving each
a name composed of two parts, both of which use Latin grammatical forms, although they can be based on
words from other languages. Such a name is called a binomial name (which may be shortened to just
"binomial"), a binomen, binominal name or a scientific name; more informally it is also called a Latin name.
The first part of the name identifies the genus to which the species belongs; the second part – the specific
name or specific epithet – identifies the species within the genus. For example, humans belong to the
genus Homo and within this genus to the species Homo sapiens. Tyrannosaurus rex is probably the most
widely known binomial.[1] The formalintroduction of this system of naming species is credited to Carl Linnaeus,
effectively beginning with his work Species Plantarum in 1753.[2] But Gaspard Bauhin, in as early as 1623, had
introduced in his book Pinax theatri botanici (English, Illustrated exposition of plants) many names of genera
that were later adopted by Linnaeus.[3]
The application of binomial nomenclature is now governed by various internationally agreed codes of rules, of
which the two most important are the International Code of Zoological Nomenclature (ICZN) for animals and
the International Code of Nomenclature for algae, fungi, and plants (ICN). Although the general principles
underlying binomial nomenclature are common to these two codes, there are some differences, both in the
terminology they use and in their precise rules.
In modern usage, the first letter of the first part of the name, the genus, is always capitalized in writing, while
that of the second part is not, even when derived from a proper nounsuch as the name of a person or place.
Similarly, both parts are italicized when a binomial name occurs in normal text (or underlined in handwriting).
Thus the binomial name of the annual phlox (named after botanist Thomas Drummond) is now written as Phlox
drummondii.
In scientific works, the authority for a binomial name is usually given, at least when it is first mentioned, and the
date of publication may be specified.

 In zoology
 "Patella vulgata Linnaeus, 1758". The name "Linnaeus" tells the reader who it was that first published a
description and name for this species of limpet; 1758 is the date of the publication in which the original
description can be found (in this case the 10th edition of the book Systema Naturae).
 "Passer domesticus (Linnaeus, 1758)". The original name given by Linnaeus was Fringilla domestica;
the parentheses indicate that the species is now considered to belong in a different genus. The ICZN
does not require that the name of the person who changed the genus be given, nor the date on which
the change was made, although nomenclatorial catalogs usually include such information.
 In botany
 "Amaranthus retroflexus L." – "L." is the standard abbreviation used in botany for "Linnaeus".
 "Hyacinthoides italica (L.) Rothm. – Linnaeus first named this bluebell species Scilla italica; Rothmaler
transferred it to the genus Hyacinthoides; the ICN does not require that the dates of either publication
be specified.
Basics of Classification (Taxonomy)
Earth today is home to more than 8 million different species. This number is constantly changing, however, as new
species are discovered at an outstanding rate. Biologists called taxonomists have devised a carefully developed scheme
to organize these myriad species. In the mid-1700s, Carolus Linnaeus, a Swedish physician and botanist, published
several books in which he described thousands of plant and animal species. Linnaeus grouped the species according to
their reproductive parts and developed the two-part binomial taxonomy system of categorizing organisms according to
genus and species. Linnaeus’s work remains valid. It has been combined with the work of Charles Darwin in the field of
evolution to form the foundation of modern taxonomy. Darwin’s theory of evolution states that all modern species are
derived from earlier species and that all organisms, past and present, share a common ancestry. Darwin’s theory of
evolution, which has become a unifying theme in biology, is the organizing principle of modern taxonomy.
Taxonomists classify organisms in a way xthat reflects their biological ancestry. Because the ancestral relationships are
complex, the taxonomic schemes are also complex and often the subject of revision. Despite their complexity, the
taxonomic schemes provide considerable insight into the unity and diversity of life. The term “classification” is
synonymous with the word “taxonomy.”
All organisms in the living world are classified and named according to an international system of criteria that dates to
the early part of the twentieth century. The rules of classification establish a procedure to be followed when a new
species is identified and named. (The rules of classification apply only to formal scientific names, not to common
names.)
The scientific name of any organism, called the binomial name, has two elements. For example, humans have the
binomial name Homo sapiens. The name of any species is two words: the name of the genus, followed by the species
modifier. For humans, Homo is the genus and sapiens is the species modifier. The genus name is generally a noun, while
the species modifier is an adjective. Thus, Homo sapiens literally translates as “human knowing” (or, more simply,
“intelligent human,” as stated in Chapter 14).

The generally accepted criterion for defining a species is that organisms of the same species interbreed under natural
conditions to yield fertile offspring. Individuals of different species normally do not mate. If they are forced to mate,
either the mating is unsuccessful or the offspring are sterile. For example, a horse (Equus caballus) can be mated to a
donkey (Equus assinus), and the result will be a mule. However, mules are sterile and cannot reproduce. Thus, the horse
and donkey are classified as different species. A quarter horse and a thoroughbred can mate and produce a fertile
offspring. Therefore, both are classified as the same species: Equus caballus.

For humans, there is only one living species: Homo sapiens. However, in past ages, other species, such as Homo
erectus, may have coexisted with Homo sapiens. Homo erectus (see Chapter 14) is considered a separate species
because presumably it could not mate with Homo sapiens.

The classification scheme provides a mechanism for bringing together various species into progressively larger groups.
Taxonomists classify two species together in the same genus (the plural is genera). For example, the horse Equus
caballus and the donkey Equus assinus are both placed in the genus Equus. Similar genera are brought together to form
a family. Similar families are classified within an order. Orders with similar characteristics are grouped in a class. Related
classes are grouped together as divisionsor phyla (the singular is phylum). Divisions are used for plants and fungi, while
phyla are used for animals and animal-like organisms. The largest and broadest category used to be the kingdom, but
this has been usurped by the taxonomic category domain.

The classification of a human shows how the classification scheme works. Working from the top down, the human is
classified first in the domain Eukarya because it is composed of eukaryotic cells. Next is kingdom Animalia because it has
the properties of animals. Animals are then divided into at least 38 phyla, one of which is Chordata. Members of this
phylum all have backbones at some time in their lives.

Members of the phylum Chordata are then subdivided into various classes. Humans belong to the class Mammalia,
together with other mammals (all of which possess mammary glands and nurse their young). The Mammalia are then
divided into several orders, one of which is Primata. Humans belong to the order Primata along with other primates,
such as gorillas and monkeys. The order Primata is subdivided into several families, one of which is Hominidae, the
family that includes humans and humanlike creatures. Within the family of Hominidae is the genus Homo, which
includes several species. One of these species is Homo sapiens.
Taxonomy is the field of biology which deals with the nomenclature, identification, and classification of organisms. There
are over one million known species on Earth and probably several million more not yet identified. Taxonomists are
responsible for identifying, naming, and classifying all these different species. Systematics is a discipline of biology that
explicitly examines the natural variation and relationships of organisms, and which includes the field of taxonomy.
Systematics also deals with the relationships of different groups of organisms, as most systematicists strive to construct
natural classification systems reflecting evolutionary relationships. Many biologists use the terms taxonomy and
systematics interchangeably.

Phenetics

Phenetics, also known as numerical taxonomy, was proposed by Sokal and Sneath in the 1950s. Although very few
modern taxonomists currently use phenetics, Sokal and Sneath's methods clearly revolutionized taxonomy by
introducing computer-based numerical algorithms, now an essential tool of all modern taxonomists.

Phenetics classifies organisms based on their overall similarity. First, many different characteristics of a group of
organisms are measured. These measurements are then used to calculate similarity coefficients between all pairs of
organisms. The similarity coefficient is a number between 0 and 1, where 1 indicates absolute identity, and 0 indicates
absolute dissimilarity. Finally, the similarity coefficients are used to develop a classification system.

Critics of phenetic classification have argued that it tends to classify unrelated organisms together, because it is based
on overall morphological similarity, and does not distinguish between analogous and homologous features. Pheneticists
have responded that they ignore the distinction between analogous and homologous features because analogous
features are usually numerically over-whelmed by the larger number of homologous features. Most evolutionary
biologists would consider this response questionable, at best.

Cladistics

Cladistics is a method that classifies organisms based on the order in which different evolutionary lines branch off from
one another. It was first proposed in the 1950s by Willi Hennig, a German entomologist. Subsequently, many other
scientists have made Hennig's original method more practicable by developing various cladistic numerical algorithms,
some of which are very sophisticated. Cladistics is currently the most widely used method of classification.

One might reasonably ask: how can cladistics possibly determine the branching points of different evolutionary lines,
given that we never have a complete fossil record and often have only living species for constructing a classification
system? The answer is that cladistics relies upon the fact that all new species evolve by descent with modification. In
other words, cladistics determines the evolutionary branching order on the basis of shared derived characteristics. It
does not use shared primitive characteristics as a basis for classification, since these may be lost or modified through the
course of evolution. To establish which characters are primitive and which are derived, cladistic classification generally
relies upon one or more outgroups, species hypothesized to be primitive ancestors of all the organisms under study.

An example illustrates the distinction between shared derived and shared primitive characteristics in cladistic
classification. The common mammalian ancestor of humans, cats, and seals had five digits on each hand and foot. Thus,
the presence of five digits is a shared primitive characteristic and cladistics does not segregate humans and cats, which
have five digits on their hands and feet, from seals, which have flippers instead of distinct digits. Instead, cladistics
classifies seals and cats in the order Carnivora, based on certain shared derived characteristics of the Carnivora, and
humans in the order Primata, based on other derived characteristics of the Primates.

It is important to note that a cladistic classification is not based on the amount of evolutionary change after the
branching off of an evolutionary line. For example, although chimps and orangutans appear more similar to one another
then either does to humans, cladistic classification places humans and chimps together since they share a more recent
common ancestor than chimps and orangutans. Such a classification may seem counterintuitive; however, cladistic
taxonomists would argue that such classifications should be considered the starting point for subsequent comparative
studies. Such comparative studies might seek to discover why human morphology evolved so rapidly, relative to that of
chimps and orangutans.

Some botanists have noted a limitation of cladistics, in that it does not recognize the role of interspecific hybridization in
the evolution of new species. In interspecific hybridization, two different species mate and produce offspring that
constitute a new species. Certain derived features of the parent species revert to primitive features in the
new hybrid species. Hybrid species appear to be more common among plants than animals, but taxonomists who study
any group of organisms clearly need to account for the possibility of interspecific hybridization in the evolution of new
species.

W. H. Wagner, a noted plant taxonomist, has shown that interspecific hybridization has had a particularly important role
in the evolution of ferns. He has advocated the development of a new methodology he calls reticulistics, to account for
the evolution of hybrid species. In reticulate phylogeny, one evolutionary line can split to form two new species or two
evolutionary lines can join together to form one new species. Unfortunately, there are not yet any numerical algorithms
that can be used to reconstruct a reticulate phylogeny.

Evolutionary taxonomy

Evolutionary taxonomy can be considered a mixture of phenetics and cladistics. It classifies

organisms partly according to their evolutionary branching pattern and partly according to the
overall morphological similarity. Evolutionary taxonomy is basically the method used by the early
evolutionary taxonomists and is also called classical taxonomy.

The major limitation of evolutionary taxonomy is that it requires a highly arbitrary judgment
about how much information to use for overall similarity and how much information about
branching pattern to use. This judgment is always highly subjective, and makes evolutionary
taxonomy a very poor method of classification, albeit one that survives in the hands of certain
older taxonomists.

Five kingdom system

According to the five kingdom system designated by L. Margulis and K. V. Schwartz, all organisms
are classified into one of five kingdoms: Monera, single-celled prokaryotes (bacteria); Protista,
single-celled eukaryotes (algae, water molds and various other protozoans); Fungi, multicellular
eukaryotic organisms which decompose organic matter (molds and mushrooms); Plantae,
multicellular eukaryotic photosynthetic organisms (seed plants, mosses, ferns, and fern allies);
and Animalia, multicellular eukaryotic organisms which eat other organisms (animals).

Clearly, the five kingdom system does not segregate organisms according to their evolutionary
ancestry. The Monera and Protista are single-celled organisms only distinguished by their
intracellular organization. The Animalia, Fungi, and Plantae are distinguished by their mode
of nutrition, an ecological, not a phylogenetic, characteristic. Plants are considered producers, in
that they use photosynthesis to make complex organic molecules from simple precursors and
sunlight. Fungi are considered decomposers, in that they break down the dead cells of other
organisms. Animals are considered consumers, in that they primarily eat other organisms, such as
plants, fungi, or other animals.

More recently, a six kingdom model has been widely, although not universally, accepted. In this
system, the former kingdom Monera is divided into two
kingdoms: Eubacteria and Archaebacteria. The eubacteria (or true bacteria) are more common
species of bacteria. Free-living decomposing bacteria, pathogenic (or diseasecausing) bacteria,
and photosynthesizing cyanobacteria belong to this group. Some familiar members of Eubacteria,
then, would be the bacteria found on human skin that can cause acne, or the bacteria found in a
compost pile, which facilitate decomposition of organic material.

The Archaebacteria (or ancient bacteria) are quite different. Members of this group of bacteria
live in very hostile environments. Examples are those living in extremely warm environments
(called thermophiles) and bacteria living in extremely salty environments (called halopohiles).
Archaebacteria are believed to be representative "living ancestors" of bacteria that inhabited the
earth eons ago. The Archaebacteria are so fundamentally different from other bacteria that the
new taxonomy reflects this difference by assigning them their own kingdom. Archaebacteria are
believed to be the most primitive organisms found on earth.

Alternative systems

Many cladistic taxonomists have criticized Whittakers five kingdom classification system because
it is not based on the branching pattern of evolutionary lineages. Cladistic classification systems
seek to place organisms into monophyletic taxa. A monophyletic taxon is one that includes all
species descended from a single common ancestor. For example, since biologists believe different
groups of multicellular animals evolved from different single-celled eukaryotic ancestors, the
kingdom Animalia is clearly not a monophyletic group.

Several cladistic taxonomists advocate a classification system that groups all organisms into three
apparently monophyletic kingdoms, the Eukaryota, Eubacteria, and Archaebacteria (alternatively
called Eukarya, Bacteria, and Archaea). The Eukaryota kingdom includes eukaryotic organisms,
and all organisms in the Plantae, Animalia, Fungi, and Protista kingdoms. The kingdoms Eubacteria
and Archaebacteria both consist of single-celled prokaryotes, all of which Whittaker placed into
the Monera kingdom. The Archaebacteria (ancient bacteria) were originally considered more
primitive than the Eubacteria. The Archaebacteria includes the methanogens (methane-producing
bacteria), halophiles (salt-loving bacteria), and thermophiles (heat-loving bacteria), all rather
unusual prokaryotes which live in very unusual habitats.

Many cladistic taxonomists are currently studying the relationships of the Eubacteria,
Archaebacteria, and Eukaryota, and have proposed different classification schemes based on
comparisons of different gene sequences of these organisms. Ironically, although Archaebacteria
acquired their name because they were considered primitive to Eubacteria, many taxonomists
now believe that Archaebacteria are in fact more modern and more closely related to the
Eukaryota than are the Eubacteria. Some taxonomists have proposed a fourth kingdom called the
Eocytes, a group of hyperthermophilic bacteria which other biologists include within the
Archaebacteria. One of the most intriguing recent studies found that Eukaryota have some genes
that are most like those in Archaebacteria and other genes most like those in Eubacteria. This
suggests that the Eukaryota may have evolved as a chimera of some primitive Eubacterium and
Archaebacterium.

Taxonomists who are intrigued by this controversy are encouraged in knowing there are many
undiscovered species of bacteria, perhaps millions, and only a very small portion of Eubacterial,
Archaebacterial, and Eukaryotal DNA sequences have been studied to date.