25/10/2013 DM-1: Lesson 9.

METHODS OF CLASSIFICATION

FUNDAMENTALS OF MICROBIOLOGY
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Module 3. Microbial taxonomy

Lesson 9
METHODS OF CLASSIFICATION

9.1 Introduction
9.1.1 Phenotypic (phenetic) classification
9.1.2 Phylogenetic (phyletic) classification
9.2 Phylogeny from Phenotype
9.2.1 Molecular phylogeny
9.3 Numerical Taxonomy
9.4 All Species Inventory
9.5 Discovery of New Microorganisms in the Stratosphere

9.1 Introduction
Two common approaches used in biological world are referred to as phenotypic and
phylogenetic classification.

9.1.1 Phenotypic (phenetic) classification

Phenotypic classification is concerned with grouping individual species into phenotypic

categories (taxons) based on how organisms ‘look’. In the recent past, taxonomists were
not equipped to classify beyond the level of phenotypic groupings except via inference
from phenotypic similarities. Phenotypic similarity and evolutionary relationship do not
always map one to one upon each other. This approach is guided by a set of morphological
and biochemical tests, constituting the cornerstone of ‘Determinative Microbiology’.

Limitations: From the standpoint of many areas of microbiology, a determinative

classification is sufficient. For example, in clinical microbiology the identification of
organisms permits the physician to assess pathogenicity and to select a treatment. In this
context, the purely determinative nature of a classification is not crucial. If the organism
has previously been described and hence is already in the classification, then it can be
identified and treated. However, from a biological point of view, the lack of a natural
system does not permit the projection of properties of previously described organisms onto
new ones that might be closely related, but not identical, to those known before. In
addition, it does not help us understand an organism that we have been unable to cultivate
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in the laboratory. Finally, it does not permit studies of the origin and evolution of cellular
functions (e.g. drug resistance, aerobiosis or photosynthesis), because there is no
evolutionary (historical) framework.

9.1.2 Phylogenetic (phyletic) classification

Phylogenetic classification is concerned with grouping individual species into evolutionary

categories. Since the early 1980s, phylogenetic classfication has been made much more
facile by the invention of molecular taxonomy. The evolutionary classification of
organisms is based on the nucleotide sequence divergence at individual loci (genes).

9.2 Phylogeny from Phenotype

These two approaches (phenotypic and phylogenetic classification) often fully match. This
is because there is usually a correlation between evolutionary relatedness and phenotypic
relatedness. However, such things as convergent evolution can create confusion between
the two classification philosophies since convergent evolution, by definition, produces
phenotypic similarity in the absence of close evolutionary relatedness. The trick to solving
these discrepancies is to concentrate on true homologies and ignore convergence. Conflicts
between phenotypic and phylogenetic classification are at the root of the various
monophyly-paraphyly debates.

9.2.1 Molecular phylogeny

A homology is a similarity between two organisms that exists because the two organisms
are closely evolutionarily related (that is, the feature in question existed in the common
ancestor to the two organisms). The similarity of the DNA (or RNA) of organisms may be
determined by a number of means including determinations of base composition,
nucleotide sequence, or DNA hybridization rates. Typically these means include very
powerful ways by which organisms may be classified, either in terms of distinctions
between organisms (i.e. the organisms may be classified as representing two or more
species) or similarities (i.e. it may be concluded from evidence of genotypic similarity that
the organisms are closely related, i.e. evolutionarily related); the latter similarities we would
classify as a genetic homology. The downside of genetic homology is that the acquisition
of data often requires a laboratory and at least a little effort. The upside is that genetic
homology describes evolutionary relationships with only minimal interference from
phenotype.

9.3 Numerical Taxonomy

It is a classification system in biological systematics which deals with the grouping by

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numerical methods of taxonomic units based on their character states. It aims to create a
taxonomy using numeric algorithms like cluster analysis. The concept was first developed
by Robert R. Sokal and Peter H. A. Sneath in 1963. Phenetics is a closely related
discipline and draws heavily from the methods of numerical taxonomy.

Although intended as an objective classification method, in practice the choice and

weighing of morphological characteristics is often guided by available methods and
research interests. Furthermore, the general consensus has become that the taxonomic
classification should reflect evolutionary (phylogenetic) processes. Some connections
between phylogenetic trees and the spectral decomposition of the variance-covariance
matrix of quantitative traits subject to Brownian motion over time have been established,
providing a theoretical link between phylogenetic methods and numerical taxonomy. The
specific phenetic algorithms proposed in numerical taxonomy, however, often fail to
properly reconstruct the phylogenetic history of organisms.

9.4 All Species Inventory

In 2001 an international project was launched to identify and record every species on earth
in the next 25 years. It is a very challenging undertaking considering that to date 1.5 million
organisms have been named. It is estimated that anywhere from 7 – 100 million living
species exist.

9.5 Discovery of New Microorganisms in the Stratosphere

On March 18th, 2009, three new species of bacteria, which are not found on earth and
which are highly resistant to ultra-violet radiation, were discovered in the upper
stratosphere by Indian scientists. The new species have been named as:

Janibacter hoylei, after the distinguished astrophysicist Fred Hoyle

Bacillus isronensis recognizing the contribution of Indian Space Research
Organization (ISRO) in the balloon experiments which led to its discovery
Bacillus aryabhata after India’s celebrated ancient astronomer Aryabhata and also
the first satellite of ISRO.

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