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Lecture1 Microbial Taxonomy

The document discusses four main systems of biological classification: artificial, natural, phylogenetic, and phenetic. It provides details on each system including examples and describes how cladistics and molecular data are used in modern systematics.

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Jonathan Nathan
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20 views

Lecture1 Microbial Taxonomy

The document discusses four main systems of biological classification: artificial, natural, phylogenetic, and phenetic. It provides details on each system including examples and describes how cladistics and molecular data are used in modern systematics.

Uploaded by

Jonathan Nathan
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Classification Systems

Systems of Biological Classification :


There are four different systems of classification, mainly used
by taxonomists:
1. Artificial System
2. Natural System
3. Phylogenetic System
4. Phenetic System
Classification Systems
1. Artificial System :
A classification based on one or a few superficial similarities.
Adopted by Pliny (first century AD)
Examples;
For animals on the basis of habitats, e.g., land, air and water.

For plants on the basis of habit into (i) herbs (ii) under shrubs
(iii) shrubs and (iv) trees. Linnaean system also used stamens-
number, length, arrangement of stamens and certain other
characters of stamens 'Genera Plantarum' (1737).

Example Linnaeus proposed classes:


Monandria ( 1 stamen),
Diandria (2 stamens) and
Tri- and polyandria ( 3 and more stamens).
2. Natural System :
A natural system of classification compares many characteristics. This
increases the amount of information available from the grouping.

A natural system of classification indicates taxonomic position and


relatedness.

It is based on morphology and evolution and is used nowadays. The


most important criterion used for the present day classification of
living organisms is based on anatomical and physiological
characteristics.

Example:
Natural system of classification of the seed plants was proposed by
George Bentham (1800-1884) and Joseph Dalton Hooker (1862-1883).

Bentham and Hooker published three volumes of "Genera Plantarum"


describing 202 families of angiosperms.
3. Phylogenetic System:
The classification based on evolutionary sequence and the genetic
relationships among the organisms. Proposed by Adolf Engler (1844-
1930)

Phylogenetic classification is based on common evolutionary descent.


Groups reflect genetic similarity and evolutionary relatedness.
Example: -organisms based on shared evolutionary heritage.
-based on RNA fingerprints and
-sequences

“Taxonomy without phylogeny is similar to bones without flesh”


is the statement of A.L. Takhtajan (1967) who wrote the book "A System
of Phylogeny of Flowering Plants".

A modern method of classification called cladistics is based on


evolutionary history. To identify groups sharing recent common
ancestry, many biologists use a procedure called cladistics.
Cladistics:
A biological classification system which categorize organisms based on
shared traits.
Organisms are typically grouped by how closely related they are and
thus, cladistics can be used to trace ancestry back to shared common
ancestors and the evolution of various characteristics.
Phylogenies are established by what distinctive features their
members share to the exclusion of more distantly related organisms.
Thus, if one wants to identify some subgroup of eg, insects, features
that all insects have in common, like six legs and segmented bodies,
are useless. One has to use features or combinations of features that
only that subgroup has.
Cladistics:

• Cladistics theory creates clades of organisms that are represented with the
help of a cladogram.
• A clade is a group of organisms that includes an ancestor and its
descendants.
• Types of clades:
Clades are of these three types:
ØMonophyletic: monophyletic clades means a group of organisms with a
single clade in it. Here you will find only one ancestor for many
descendants.
ØParaphyletic: this clade includes an ancestor and multiple descendants.
ØPolyphyletic: in this clade, organisms possess homoplasy traits. It means
organisms in a group show similar characteristics, but they don’t relate.
Examples of clades
Phylogeny vs cladistics
Phylogeny Cladistics
Represents the historical evolutionary relationship of Deals with the recent ancestor and descendants
organisms relationship of organisms.
Involves making groups with the help of physical Talks about the actual traits of the organisms.
characteristics of organisms

Is done with the help of a phylogenetic tree Representation is done using a cladogram.
What kind of molecular data do we use in systematics?
Nowadays, mostly DNA sequence data are used because:

• it is comparably inexpensive. The cost per sequenced base from


purified PCR-product is roughly $ 5.

• The information source is almost inexhaustible. Most organisms


contains billions of DNA bases (Homo sapiens 3.2 x109).

• Typical studies in systematics consists of a few regions containing


1000-3000 bases.
Every position in an aligned DNA sequence matrix is a character.
-You donʼt code characters, like in morphology.
-Many characters are constant, but still included
-Although there might be many characters, some do not carry much
information.
• Are DNA regions for phylogenetic inference an unbiased sample?
• No!
• Heavy reliance on “popular” regions.
• Some use mtDNA, others use nrDNA. There is thus Limited usage of
“real” nuclear regions.

How come?
Choosing a molecular mark depends on:
• -GenBank accessions and availability.
• Primer construction,
• -No gene-family problems- less problems with heterozygosity
• people likes direct sequencing which do not involve cloning.

• Fast evolving regions could be useful for inferring relationships


between closely related taxa.
• Highly conserved regions (e.g. metabolically important genes) could
be “better” for distantly related taxa, and are more likely to be found
in many organism groups.
4. Phenetic System :
Phenetic System taxonomy (classification) is based on the
overall similarity of organisms evaluated without regard to
phylogeny. It is based on observable characteristics of
existing organisms .

Phenetic System taxonomy is based upon expressed


characteristics, where by groups do not necessarily reflect
genetic similarity or evolutionary relatedness. Instead,
groups are based on convenient, observable
characteristics. Groups of organisms are based on mutual
similarity of phenotypic characteristics

Phenetic classification did not have a strong impact on


animal classification and scientific interest in this
approach it is now in decline.
Phenetic System..
It is also referred to as Phenotypic taxonomy/ -
“conventional taxonomy”
groupings of organisms based on mutual similarity of
phenotypic (physical and chemical) characteristics.
Numerical Taxonomy: a common approach to phenetic
taxonomy
-It employs a number of phenotypic characteristics to
generate similarity coefficients that may be mapped in
dendrograms.
Phenetic groupings based on numerical taxonomy may or
may not correlate with evolutionary relationships
Dendrograms: is a diagram that shows the hierarchical
relationship between objects. Is a tree-like diagram used to
show the ancestors and descendants of species
Others but not popular
i. New Systematics :
Sir Julian Huxley (1940) proposed the term ʻNew systematicsʼ as follows:
• Cytotaxonomy - based on cytological study.
• Karyotaxonomy - based on nucleus and chromosomes.
• Morphotaxonomy - based on morphological characters.
• Biochemical taxonomy - based on biochemical studies.
• Chemotaxonomy - based on specific chemicals like secondary
metabolites.
• Numerical taxonomy - based on statistical methods.
• Experimental taxonomy - based on experimental - determination of
genetical interrelationships and role of environment in their formation

ii. Polyphasic taxonomy – mixed


assembles and assimilates many levels of information from
molecular to ecological.
It is new but - fast.

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