CORE PAPER-I: BIOSYTEMATICS, ANIMAL BIODIVERSITY AND

PHYLOGENY
UNIT-I

Definition, basic concept and importance of

Systematics and Taxonomy

Taxonomy
Variation is the rule of nature. The most impressive aspect of the world of life is its diversity
and the uniqueness of its components. No two sexually reproducing populations are the same,
nor are any two populations, species or higher taxa. About more than one million species of
animals and half a million of plants have already been described and estimates on the number
of still undescribed living species ranges from three to ten millions. Furthermore each species
may exist in numerous different forms like sexes, age, seasonal forms, morphs etc. It would be
impossible to deal with this enormous diversity if it were not ordered and classified. Systematic
Zoology endeavors to order this diversity of the animal world and to develop methods and
principles to make this task possible.
Definition of taxonomy
Taxonomy is the theory and practice of identifying plants and animals. In fact, taxonomy deals
with the principles involved in the study of classification of organisms. It is the functional
science which deals with identification, nomenclature and classification of different kinds of
organisms all over the world. The word ‘taxonomy’ is derived from the Greek
words taxis (=arrangement) and nomos (=law). The term ‘taxonomy’ was coined by A.P. de
Candolle in 1813. Different workers have tried to define taxonomy from their view point. Some
of the accepted definitions of taxonomy are as follows:
· According to Mason (1950) taxonomy is the synthesis of all the facts about the organisms into
a concept and expression of the interrelationship of organisms.
· Harrison (1959) defined taxonomy as the study of principles and practices of
classification, in particular in methods, the principles and even in part, the result of biological
classification.
· Simpson (1961) defines taxonomy as the theoretical study of classification, including
its bases, principles, procedures, and rules.
· Heywoods (1967) defined taxonomy as the way of arranging and interpreting
information’s.
· Blackwelder (1967) explains it as the day to day practice of handling different kinds of
organisms. It includes collection and identification of specimens, the publication of data, the
study of literature and the analysis of variations shown by the specimens.· According to
Johnson (1979), taxonomy is the science of placing biological form in order.
· Christoffersen (1995) defines taxonomy as the practice of recognizing, naming and
ordering taxa into a system of words consistent with any kind of relationships among taxa that
the investigator has discovered in nature.
Systematics
Systematics is the study of diversification and relationships of life forms of extinct extant.
The word systematics is derived from the Latinized Greek word ‘systema’ applied to the
system of classification developed by Linnaeus in the 4th edition of his historical
book Systema Nature in 1735. Today’s systematics generally makes extensive use of
molecular biology and computer Programs to study organisms.
Definition of systematic
· According to Blackwelder and Boyden (1952), “systematic is the entire field dealing
with the kind of animals, their distinctions, classification, and evolution.
· Simpson (1961) defines systematic as “The scientific study which deals with kinds and
diversity of organisms and any or all relationships among them’
· According to Blackwelder (1967), systematics is that science which includes both
taxonomy and classification, and all other aspects of dealing with kinds of organisms and the
data accumulated about them.
· Christofferson (1995) defined systematic as the theory, principles and practice of
identifying (discovering) systems, i.e., of ordering the diversity of organism (parts) into more
general systems of taxa (wholes) according to the most general causal processes.
· According to Padian (1999), systematic can be seen as the philosophy of organization
nature, taxonomy as the use of sets of organic data guided by systematic principles, and
classification as the tabular or hierarchical end result of this activity.
Relationship of taxonomy to the systematics
Kapoor (1998) considered that the relationship of taxonomy to systematics is
somewhat like that of theoretical physics to the whole field of physics. Taxonomy includes
classification and nomenclature but systematics includes both taxonomy and evolution. In
simple terms, actually there are two parts of systematic. The first part, taxonomy, is
concerned with describing and naming the different kinds of organisms, whether exist or
extinct. This science is supported by institutions holding collection of organisms which are
curated with relevant data. The second part of systematics, evolution, is concerned with
understanding just how all these kinds of animals arose in the first place and what processes
are at work today to maintain or change them. Systematics uses taxonomy as a means to
understand organisms. Systematics elucidate the new methods and theories that can be used
to classify species based on similarities of traits and possible mechanisms of evolution, a
change in gene pool of a population over time. According to Wagele (2005), although
theoretically the term taxonomy and systematic could be synonyms, in practice, however,
differences in uses are obvious and a systematist and a taxonomist can conduct different
analyses.
The major differences between taxonomy and systematic can be summarized as
follows:
1. Taxonomy is the most important branch of systematic and thus systematics is a broader
area than taxonomy.
2. Taxonomy is concerned with nomenclature, description, classification and identification
of a species, but systematics is important to provide layout for all those taxonomic
functions.
3. Evolutionary history of a species is studied under systematics but not in taxonomy.
4. The environmental factors are directly related with systematics but in taxonomy it is
indirectly related.
5. Taxonomy is subjected to change in course of time, but systematics is not changed if
it was properly done.
Stages in taxonomy
There are several stages of taxonomy such as:-
1. Alpha taxonomy:- In this stage species are identified and characterized on the basis
of gross morphological features.
2. Beta taxonomy:- In this stage species are arranged from lower to higher categories,
i.e., hierherarchic system of classification.
3. Gamma taxonomy:- In this stage intraspecific differences and evolutionary history
are studied.
Classical Taxonomy and Modern Taxonomy:
Classical Taxonomy:
The classical taxonomy is based on observable morphological characters with normal
individuals considered to be expression of the same while their variations are believed to
be imperfect expressions. Classical taxonomy originated with Plato followed by Aristotle
(Father of Zoology), Theophrastus (Father of Botany) up to Linnaeus (Father of Taxonomy)
and his contemporaries.
1. Species are delimited on the basis of morphological characteristics.
2. Only a few characters are employed for classification.
3. A few individuals or their preserved specimens are used for study. It is called
typological concept.
4. Species are believed to be static.
5. Species is the centre stage of study. Its subunits are not important.
Modern Taxonomy (New Systematics):
The term new systematic was coined by Julian Huxley (1940). New systematic is
systematic study which takes into consideration all types of characters. Besides classical
morphology, it includes anatomy, cytology, physiology, biochemistry, ecology, genetics,
embryology, behavior etc. of the whole population instead of a few typological specimens.
In contrast classical systemetics is based on the study of mainly morphological traits of one
or a few specimens with supporting evidences from other fields. New systematics ia also
called population systematics and biosystematics. It strives to bring out evolutionary
relationship amongst organisms.
1. New systematic is based on the all types of variation in the species.
2. Along with morphological variations, other investigations are also carried out to know
the variety of traits.
3. Delimitation of species is carried out on the basis of all types of biological traits. It is
also called biological delimitation.
4. Traits indicating primitiveness and advancement are found out.
5. Inter-relationships are brought out.
6. Species are considered as dynamic unit.
Aims and tasks of taxonomist:-
The various aims and tasks of a taxonomist are-
1. To catalogue and preserve the biodiversity collected from different sources.
2. To differentiate the variations among organisms and arranged them on the basis of
their relationships or associations.
3. To provide scientific name to the taxa, so that one can recorded, stoe and retrieved
when needed.
4. To establish a set of rules to choice characters for arranging species into hierarchic
classification.
5. To study the genetic and phylogenetic relationships among life forms.
6. To make extensive use of computer to analyze and differentiate the intra and
interspecific relationships among organisms.
The contribution of systematic to biology:
Systematics is the key to understand fascinating biodiversity around us. Systematics
benefits the human beings by providing the fundamental knowledge about the sustainable
resource management, environmental protection, and landscape preservation to food
security. Systematic biology provides the skill to make policies for successful
implementation of preservation and management of our biodiversity, which is critical to
have long term quality of life for us as well as to our nature.
The contribution of systematic to biology can be studied into two heads:-
A. Theoretical biology and
B. Applied biology.
A. Theoretical biology:-
Systematics has played some important role in the field of theoretical biology, such
as:-
1. It is responsible in making conceptual contribution like population thinking.
2. It is responsible in solving the problems of multiplication of species. It illustrates the
structure of species and evolutionary processes.
3. Mimicry and other evolutionary areas also have been a clearly understood through
taxonomy.
4. It has also played important role in the development of behavioural science.
5. Taxonomy is the key to the study of ecology, as no ecological survey can be
undertaken unless all the species of ecological importance are identified.
B. Applied biology:-
Systematics provides basic understanding about the components of biodiversity which is
necessary for effective decision making about conservation and sustainable use. The most
important are:-
1). Agriculture and forestry: - Presently we are faced with the acute problem of saving
our crops and trees from the attack of various kinds of pests. So, it is necessary to know the
correct names of such pests; before their proper control, and eradication. Taxonomists can
give correct identification of pest species, which is vital for its effective control. Similarly,
many of the plant diseases are caused by certain vectors. The correct identification of a
particular vector is vital for bringing the vector under control by killing its transmitters.
2). Biological control: - Natural enemies of pests can be introduced for biological
control of pests. The biological control is much more economical than the chemical control.
In 1940s a parasite Archytus incertus was introduced from Uruguay and Argentina into
the U.S.A. to control armyworms. The sytematists are presently greatly involved in
designing and implementing the biological contol programmes of pests and diseases most
effectively.
3). Public health: - Taxonomy plays an important role in public health program
also. There are number of diseases, which are spread by many Arthropods. So, our
controlled measures should be planned to attack the target species. As for example,
All Anopheles maculipennis are not responsible for transmitting malaria. This species
consists of several sibling species, of which a few were responsible for transmitting malaria.
An expert taxonomist can identify this particular sibling species. A correct identification
ensures a maximum of effective control at minimum cost.
4). Quarantine: - Many new pests and diseases of plants, animals and human beings
can spread from one country to another through transportation. Respective Governments
have established quarantine laboratories at aerodromes, ports etc. to check such
transmissions. Taxonomists play a vital role here in prompt identification of these pests and
diseases.
5). Wild life management: -Presently great attention is being paid to conserve and
propagate wild life. The indiscriminate killing and felling of trees have already resulted in
great disturbance in the natural environment. Taxonomists can help all environmental
protectors by identifying the economically and ecologically important wild life. The task is
important for the preservation and protection of our biodiversity.
6). Mineral prospecting: -The identification of fauna and flora in sedimentary
rocks gives a clear picture of the sequence of geological events, which helps in search for
fuels and mineral deposits. The paleontologists play a major role in the identification of
such fossil specimens of the sedimentary rocks and thus give us a clear picture of the correct
sequence of geological events. Such works have been great success in the industrialization
in America.
7). National defense: - Information concerning disease vectors and parasites is an
obvious application of systematics to national defense. The use of biological means in the
war is economical and requires fewer efforts in their operation. During World War II,
Japanese paper balloons carrying paper balloons created havoc in the forest of north east
America. Eventually a balloons was recovered with sand contained a large number of shells
of micro-organisms. The taxonomists of America observed the shells of micro-organisms
and confirmed that this type of sand represent mainland island of Japan. Subsequent
bombing of this beach area destroyed the balloon launching site. Moreover, the
identification of potential disease vectors is vital to the health of both military and civilian
populations all over the world.
8). Environmental problem: - Taxonomists have played an important role in
detecting some of the environmental problems. Certain pesticides are entered in the food
chain of ecosystem and biomagnification of pesticide takes place at certain trophic level.
Here a taxonomist can play important role in detecting such problem and can take effective
measures to control it. Presently water pollution is considered as a major environmental
problem. Certain planktons are reliable indicator of the degree of water pollution. The
identification of such organism by taxonomoists give rapid information for detecting
pollution.
9). Soil fertility: - Some organisms play important role in increasing the fertility of
soil. So, it is necessary to know such animals for their proper management in agriculture.
 10). In commerce: - Many animals and animal’s products are used commercially
by human beings such as, - honey, silk, lac, dyes etc. Systematics play important role in
increasing and improving the qualities of these products by manipulating the useful species.
Systematists and taxonomists are presently employed by universities, research
institute, museum, central and state govt. agencies,
industries, and zoos. A well trained taxonomist is well qualified teacher to teach
course of zoology or biology as he has a great
background in morphology, physiology, genetics and ecology.
Importance of Biosystematics:
The importance of biosystematics in biology can be briefed as under –
1. Biosystematics gives us a vivid picture of the existing organic biodiversity of our
earth.
2. It provides much of the information permitting a reconstruction of the phylogeny of
the life.
3. It reveals numerous evolutionary phenomena and thus makes them available for casual
study by the other branches of biology.
4. It supplies, almost exclusively, the information needed for entire branches of biology.
5. It is indispensable in the study of ecologically and medically important organisms.
It supplies classifications which are of great heuristic and explanatory value in most
branches of biology like evolutionary
biology, biochemistry, immunology, ecology, ethology and historic
HISTORY OF NOMENCLATURE
 International Code of Zoological
Nomenclature (ICZN)

Brief History of International Code of Zoological Nomenclature:

The need for a code to give a scientific name to every species was first realized
by British Association for the Advancement of Science in 1842, when a set of rules
were framed by it. This was also felt by American Association for the Advancement
of Science in 1877. Then similar learned bodies in different countries like France,
Germany and Soviet Union developed codes for their respective countries.

In 1889, at the International Congress of Zoology in Paris, discussions were made to

find out some common code of nomenclature. First version of the code .was adopted
in the Vth International Congress of Zoology in Berlin in 1901. In the XV th session
held in London in 1958, the codes were rewritten and published on 6 th November,
1961 and the updated version of the code (1961) was made available in 1964 (2nd
edition).
This code is concerned only up to naming of superfamily and did not satisfy the
zoologists. The latest edition (4th edition) of the code was published in 1999 and its
effective use has started from 2000.
The International Zoological Congress elects a judicial body, called International
Commission of Zoological Nomenclature which interprets or recommends the
provisions of the code for classification or nomenclatural problems of the animals.

Again the International Code of Zoological Nomenclature (ICZN) formed by the

International Commission of Zoological Nomenclature to see the rules and principles
of nomenclature and the application of these rules for both living and fossil animals.

Parts of International Code of Zoological Nomenclature:

The International Code of Zoological Nomenclature contains three main parts:

(i) The Code proper,

(ii) The Appendices and

(iii) The Official glossary.

The code proper includes a preamble followed by 90 articles which cover mandatory
rules without any explanation.

There are three Appendices, of which the first two cover the status of
recommendations and the third part of the Appendices is the constitution of the
commission. The glossary contains the terms used in the codes with detailed
definition.
Rules of Zoological Nomenclature:
At present the naming of the animal is governed by the International Code of
Zoological Nomenclature. There are many rules (Articles) concerning the Zoological
Nomenclature.

Of these rules, some important ones are cited below:

1. Zoological nomenclature is independent of other system of nomenclature. The
scientific name of animals and plants must be different, and the generic name of a
plant and an animal may be same, but this system is to be avoided. e.g., the generic
name of banyan or fig tree is Ficus and the fig shell (a kind of gastropod shell) is
Ficus. The scientific name of fig tree is Ficus carica or F. indica, etc., but the scientific
name of the fig shell is Ficus ficus or Ficus gracilis, etc.

2. The scientific name of a species is to be binomial (Art. 5.1) and a subspecies to be

trinomial (Art. 5.2).

e.g., the scientific name of Indian bull frog is Rana tigerina. It is binomial. The
scientific name of Indian lion is Panthera leo persica. It is trinomial. Such a system of
naming by three Latin or Latinised words is known as trinomial nomenclature.
Sometimes it becomes imperative to recognise subspecies within a species and is
given a third specific name.

3. The first part of a scientific name is generic (L. Genus = race) and is a single word
and the first alphabet or letter must be written in Capital letter. The genus must be a
noun in the nominative singular. The generic part assigns a Latin noun, a Latinized
Greek or a Latinized vernacular word.

4. The second part of a name is species (L. species = particular kind) name and may
be a single word or a group of words. The first alphabet or letter of the species name
must be written in small letter. The species name must be adjective form in nominative
singular agreeing in gender with genus name which is in noun form; e.g.:

The specific name (species part) indicates distinctness while generic part shows
relationship.

5. If the species names are framed after any person’s name, the endings of the species
are i, ii and ae, or if the species name are framed after geographical place, the endings
of the species are ‘ensis’, ‘iensis’, e.g.:

6. First part of a compound species-group name is a Latin letter and denotes a

character of the taxon, connected to the remaining part of the name by a hyphen (-),
e.g., Sole (a kind of flat fish)—Aseraggodes sinus-arabici. L. Sinus = recess
China-rose (a kind of coloured rose)—Hibiscus rosa-sinensis. L. rosa = rose
7. If a subgenus taxon is used, it is included within parenthesis in between genus and
species part and is not included in binomial and trinominal nomenclature, e.g.:

8. The person who first publishes the scientific name of an animal, is the original
auther of a name, may be written after the species name along with the year of
publication. The author’s name may be in its abbreviated form.

Lion—Felis leo Linnaeus, 1758 Lion—Felis leo Linn., 1758 or Felis leo L., 1758

9. Comma is only used between author’s name and the year of publication (Art. 22.
A. 2.1), e.g., the scientific name of Common octopus is Octopus vulgaris Cuvier,
1797. No punctuation marks are considered one to other ends of the name, e.g.,
“Octopus vulgaris Cuvier, 1797” (Not considered). No diacritic mark, apostrophe (i’)
and hypen (-) are used in names. In German word the umlaut sign is removed from a
vowel and the letter ‘e’ is inserted after the vowel, e.g., mulleri becomes muelleri.

10. If the original generic name given by the first author who also reported the species
name, transfers the species part from one genus to the other, the name of the original
author is put within parenthesis, e.g.,

Tiger:
Felis tigris Linnaeus, 1758. At first almost all the members of the cat family were
placed under the genus-Felis.

Later the genus Felis was divided into two genera, the genus of
the larger cats (tiger, lion, leopard, etc.) is Panthera and
smaller cats such as jungle cat, fishing cat, golden cat, etc. are
placed under the genus Felis, e.g.:

Lion—Felis leo Linnaeus, 1758 – Lion—Panthera leo (Linnaeus, 1758)

Jungle cat—Felis chaus

11. The names are not acceptable before the publication of Linnaean treatise, Systema
Naturae (10th edition) which was published on 1st January, 1758 except the Nomen-
clature of spiders which starts in 1757. The book Aranei suecici was published by C.
Clerck in 1757.
12. The scientific names must be either in Latin or Latinised or so constructed that
they can be treated as a Latin word.

13. The scientific names must be italicised in printed form, or underlined in hand
written or in typed forms, e.g.

Indian leopard—Panthera pardus fusca (Meyer)

Principle of priority:
Of all the rules of zoological nomenclature, it is the most controversial part to choose
the correct name when two or more names of a single taxon are discovered. Arbitrari-
ness in nomenclature prevails since the period from 1780-1850. The taxonomists of
different countries specially in Europe were unable to consult the names of different
taxa during the period of French revolution and Napoleonic wars.

A large number of synonyms appeared on these days. The continuous change of

names of different taxa could be prevented when priority was adopted as a basic
principle of nomenclature.
Reasons for the Changes of Name:
1. Changes dictated by scientific progress:
(i) Change of the generic part of binomial (binominal).

(ii) Change of specific name.

(iii) Synonymising of currently accepted species names.

(iv) Analysis of species complex.

2. Changes dictated by rules of nomenclature:

(i) Discovery of an earlier (senior) synonym.

(ii) Discovery of an earlier (senior) homonym.

(iii) Discovery of an earlier genotype fixation.

(iv) Discovery of inapplicable type-specimen.

The Three domains
of life
1. Define phylogeny.
2. Name the 3 Domains of the 3 Domain system of classification and recognize
a description of each.
3. Name the four kingdoms of the Domain Eukarya and recognize a description
of each.
4. Define horizontal gene transfer.

The Earth is 4.6 billion years old and microbial life is thought to have first appeared
between 3.8 and 3.9 billion years ago; in fact, 80% of Earth's history was exclusively
microbial life. Microbial life is still the dominant life form on Earth. It has been
estimated that the total number of microbial cells on Earth on the order of 2.5 X
1030 cells, making it the major fraction of biomass on the planet.

Phylogeny refers to the evolutionary relationships between organisms. The Three

Domain System, proposed by Woese and others, is an evolutionary model of
phylogeny based on differences in the sequences of nucleotides in the cell's ribosomal
RNAs (rRNA), as well as the cell's membrane lipid structure and its sensitivity to
antibiotics. Comparing rRNA structure is especially useful. Because rRNA molecules
throughout nature carry out the same function, their structure changes very little over
time. Therefore similarities and dissimilarities in rRNA nucleotide sequences are a
good indication of how related or unrelated different cells and organisms are.
There are various hypotheses as to the origin of prokaryotic and eukaryotic cells.
Because all cells are similar in nature, it is generally thought that all cells came from
a common ancestor cell termed the last universal common ancestor (LUCA). These
LUCAs eventually evolved into three different cell types, each representing a domain.
The three domains are the Archaea, the Bacteria, and the Eukarya.
Figure. A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea,
and eukaryota domains.

More recently various fusion hypotheses have begun to dominate the literature. One
proposes that the diploid or 2N nature of the eukaryotic genome occurred after the
fusion of two haploid or 1N prokaryotic cells. Others propose that the
domains Archaea and Eukarya emerged from a common archaeal-eukaryotic ancestor
that itself emerged from a member of the domain Bacteria. Some of the evidence
behind this hypothesis is based on a "superphylum" of bacteria called PVC, members
of which share some characteristics with both archaea and eukaryotes. There is
growing evidence that eukaryotes may have originated within a subset of archaea. In
any event, it is accepted today that there are three distinct domains of organisms in
nature: Bacteria, Archaea, and Eukarya. A description of the three domains follows.
 There is a "superphylum" of bacteria called PVC, referring to the three
members of that superphylum: the Planctomycetes, the Verrucomicrobia, and the
Chlamydiae. Members of the PVC, while belonging to the domain Bacteria, show
some features of the domains Archaea and Eukarya.

Some of these bacteria show cell compartmentalization wherein membranes surround

portions of the cell interior, such as groups of ribosomes or DNA, similar to
eukaryotic cells. Some divide by budding or contain sterols in their membranes, again
similar to eukaryotes. Some lack peptidoglycan, similar to eukaryotes and archaea. It
has been surmised that these bacteria migh be an intermediate step between an
ancestor that emerged from a bacterium (domain Bacteria) and an archael-eukaryotic
ancestor prior to its split into the domains Archaea and Eukarya.

The Archaea (archaebacteria)

The Archaea possess the following characteristics:

a. Archaea are prokaryotic cells.

b. Unlike the Bacteria and the Eukarya, the Archaea have membranes composed
of branched hydrocarbon chains (many also containing rings within the
hydrocarbon chains) attached to glycerol by ether linkages (Figure 1.3.31.3.3).
c. The cell walls of Archaea contain no peptidoglycan.
d. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are
sensitive to some antibiotics that affect the Eukarya.
e. Archaea contain rRNA that is unique to the Archaea as indicated by the
presence molecular regions distinctly different from the rRNA
of Bacteria and Eukarya.
Figure: Membrane Lipids of Archaea, Bacteria, and Eukarya. The Bacteria and the Eukarya have
membranes composed of unbranched fatty acid chains attached to glycerol by ester linkages. The
Archaea have membranes composed of branched hydrocarbon chains attached to glycerol by ether
linkages.

Archaea often live in extreme environments and include methanogens, extreme

halophiles, and hyperthermophiles. One reason for this is that the ether-containing
linkages in the Archaea membranes is more stabile than the ester-containing
linkages in the Bacteria and Eukarya and are better able to withstand higher
temperatures and stronger acid concentrations.

The Bacteria (eubacteria)

Bacteria (also known as eubacteria or "true bacteria") are prokaryotic cells that are
common in human daily life, encounter many more times than the archaebacteria.
Eubacteria can be found almost everywhere and kill thousands upon thousands of
people each year, but also serve as antibiotics producers and food digesters in our
stomachs. The Bacteria possess the following characteristics:

a. Bacteria are prokaryotic cells.

 b. Like the Eukarya, they have membranes composed of unbranched fatty acid
chains attached to glycerol by ester linkages (Figure 1.3.31.3.3).
c. The cell walls of Bacteria, unlike the Archaea and the Eukarya, contain
peptidoglycan.
d. Bacteria are sensitive to traditional antibacterial antibiotics but are resistant to
most antibiotics that affect Eukarya.
e. Bacteria contain rRNA that is unique to the Bacteria as indicated by the
presence molecular regions distinctly different from the rRNA
of Archaea and Eukarya.

Bacteria include mycoplasmas, cyanobacteria, Gram-positive bacteria, and Gram-

negative bacteria.

The Eukarya (eukaryotes)

The Eukarya (also spelled Eucarya) possess the following characteristics:

a. Eukarya have eukaryotic cells.

b. Like the Bacteria, they have membranes composed of unbranched fatty acid
chains attached to glycerol by ester linkages (Figure 1.3.31.3.3).
c. Not all Eukarya possess cells with a cell wall, but for those Eukarya having a
cell wall, that wall contains no peptidoglycan.
d. Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to
most antibiotics that affect eukaryotic cells.
e. Eukarya contain rRNA that is unique to the Eukarya as indicated by the
presence molecular regions distinctly different from the rRNA
of Archaea and Bacteria.
The Eukarya are subdivided into the following four kingdoms:

1. Protista Kingdom: Protista are simple, predominately unicellular eukaryotic

organisms. Examples includes slime molds, euglenoids, algae, and protozoans.
2. Fungi Kingdom: Fungi are unicellular or multicellular organisms with
eukaryotic cell types. The cells have cell walls but are not organized into
tissues. They do not carry out photosynthesis and obtain nutrients through
absorption. Examples include sac fungi, club fungi, yeasts, and molds.
3. Plantae Kingdom: Plants are multicellular organisms composed of eukaryotic
cells. The cells are organized into tissues and have cell walls. They obtain
nutrients by photosynthesis and absorption. Examples include mosses, ferns,
conifers, and flowering plants.
4. Animalia Kingdom: Animals are multicellular organisms composed of
eukaryotic cells. The cells are organized into tissues and lack cell walls. They
do not carry out photosynthesis and obtain nutrients primarily by ingestion.
Examples include sponges, worms, insects, and vertebrates.

It used to be thought that the changes that allow microorganisms to adapt to new
environments or alter their virulence capabilities was a relatively slow process
occurring within an organism primarily through mutations, chromosomal
rearrangements, gene deletions and gene duplications. Those changes would then be
passed on to that microbe's progeny and natural selection would occur. This gene
transfer from a parent organism to its offspring is called vertical gene transmission.

It is now known that microbial genes are transferred not only vertically from a parent
organism to its progeny, but also horizontally to relatives that are only distantly
related, e.g., other species and other genera. This latter process is known as horizontal
gene transfer. Through mechanisms such as transformation, transduction,
and conjugation, genetic elements such as plasmids, transposons, integrons, and even
chromosomal DNA can readily be spread from one microorganism to another. As a
result, the old three-branched "tree of life" in regard to microorganisms
(Figure 1.3.11.3.1) now appears to be more of a "net of life."

Microbes are known to live in remarkably diverse environments, many of which are
extremely harsh. This amazing and rapid adaptability is a result of their ability to
quickly modify their repertoire of protein functions by modifying, gaining, or losing
their genes. This gene expansion predominantly takes place by horizontal transfer.

Summary
1. Phylogeny refers to the evolutionary relationships between organisms.
2. Organisms can be classified into one of three domains based on differences in
the sequences of nucleotides in the cell's ribosomal RNAs (rRNA), the cell's
membrane lipid structure, and its sensitivity to antibiotics.
3. The three domains are the Archaea, the Bacteria, and the Eukarya.
4. Prokaryotic organisms belong either to the domain Archaea or the domain
Bacteria; organisms with eukaryotic cells belong to the domain Eukarya.
5. Microorganism transfer genes to other microorganisms through horizontal gene
transfer - the transfer of DNA to an organism that is not its offspring.