1.
Taxonomic Hierarchy
“This sequential
placement of more than one taxa one above the other or one inclusive of the
other is known as Taxonomic Hierarchy”.
Taxonomic
hierarchy was introduced by Carolus Linnaeus. It is the arrangement of various taxonomic
levels in descending order starting from kingdom up to species.
1. Species; is the lowest of
classification and shows the high level of similarities among the
organisms. For example, Helianthus annuus and Helianthus tuberosus.
These two species differ in their morphology. Both of them are
herbs but Helianthus tuberosus is a perennial herb.
2. Genus; consist of
multiple species which have similar characters but differ from the species
of another genus. Example: Helianthus, Tridax.
3. Family; comprises
a number of genera which share some similarities among them. Example:
Asteraceae.
4. Order; includes
group of families which show less similarities among them.
5. Class; consists of
group of orders which share few similarities.
6. Division; is the next
level of classification that consists of number of classes.
Example: Magnoliophyta.
7. Kingdom; is the
highest level or rank of the classification. Example: Plantae
These categories represent the rank to which
taxa are assigned. These taxa are (in ascending order): Species; Genus; Family;
Order; Class; Division; Kingdom; and/or even a Domain. This hierarchy principally helps us to avoid
chaos. There are thousands of organisms which have to be classified. Main ranks: Categorisation helps in providing
homogeneity to the various systems of classification.
Salient features of structure of Taxonomical
Hierarchy
· A taxonomical hierarchy consists of a number
of categories.
· A category is an abstract concept.
· A group of plants are assigned to such
categories for the purpose of classification.
· The categories are employed in a
conventional order which must be strictly adhered to.
· The level at which a category stands in the
hierarchy is known as rank.
· The group of plants themselves are known as
taxa (singular : taxon). · The
taxa
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2. Plant identification (Traditional keys)
“Keys are devices consisting of series
of contrasting statements requiring the identifier to make comparison and
decision based on statements of the key as related to the material to be
identified”.
A key is device which when properly
constructed and used enables a user to identify an organism.
There are two types of taxonomic Keys:
1.
Dichotomous keys
2.
Polyclave or multiaccess or synoptic key
1.
Dichotomous keys:
The most common type of key
is a dichotomous key. It consists of a sequence of two contrasting statements.
A pair of contrasting statements is known as couplet. Each
statement is known as lead.
The plant is correctly identified with keys by narrowing down
the characters found in plant. In constructing a key, contrasting characters
are chosen that divide the full set of possible species into smaller and smaller
groups i.e. the statements typically begin with broad characteristics and
become narrower as more choices are required.
Types of Dichotomous keys: There are two types
of Dichotomous keys. They differ in the method by which the couplets are organized
and how the user is directed to successive choices.
1. Indented Keys
(also called yoked) :Indents the choices (leads) of
the couplet an equal distance from the left margin. The user goes to the next
indented couplet following the lead that was selected.
2. Bracketed Keys: Provides both choices side-by-side. The choices of the couplet
must be numbered (or lettered). It is very helpful if the previous couplet is
given. This key has exactly the same choices as the first example. The choices
are separated. But it is easy to see the relationships. While this key might be
more difficult to construct, it gives more information to the user.
2.
Polyclave or Multi-entry key. It consists of a list
of numerous character states. The user selects all states that match the
specimen. Polyclave keys are implemented by a computer algorithm.
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3.
Herbarium
“ Herbaria are
store houses of preserved plant collections”. Plants are preserved in the form
of pressed and dried specimens mounted on a sheet of paper. Herbaria act as a
centre for research and function as sources of material for systematic work.
Preparation of herbarium Specimen
Herbarium Specimen is defined as a
pressed and dried plant sample that is permanently glued or strapped to a sheet
of paper along with a documentation label.
Preparation of herbarium specimen includes
the following steps.
1. Plant
collection: Field collection, Liquid preserved collection,
Living collection, Collection for molecular studies.
2. Documentation
of field site data
3. Preparation
of plant specimen
4. Mounting
herbarium specimen
5. Herbarium
labels.
6. Protection
of herbarium sheets against mold and insects
International
Herbarium
National
Herbarium
Uses of Herbarium
1. Herbarium
provides resource material for systematic research and studies.
2. It
is a place for orderly arrangement of voucher specimens.
3. Voucher
specimen serves as a reference for comparing doubtful newly collected fresh specimens.
4. Voucher
specimens play a role in studies like floristic diversity, environmental
assessment, ecological mechanisms and survey of unexplored areas.
5. Herbarium
provides opportunity for documenting biodiversity and studies related to the
field of ecology and conservation biology.
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4.
Floras
‘Flora is the
document of all plant species in a given geographic area. Flora consists of
total number of plant species in an area and gives information about flowering
season, fruiting season and distribution for the given geographic area.
It also provides
details on rare and endemic species of that area. Example: Flora of Tamil Nadu
Carnatic by K.M.Matthew. Floras are categorized based on the scope and area
covered.
1.Local Flora :It covers the limited areas, usually state,
country, city or mountain range. Example: ‘Flora of Thiruvannamalai District’
by R. Vijaysankar, K. Ravikumar and P. Ravichandran.
2.Regional
Flora: It includes large geographical area or a
botanical region. Example: ‘Flora of Tamil Nadu’ Carnatic by K.M.Matthew (1983),
‘Flora of Madras Presidency’ by J.S. Gamble and Fischer.
3.Continental
Flora: This flora covers the entire continent.
Example: ‘Flora
of Europaea’ by D.A.Web.
4.Electronic
Floras (e - floras): It is nothing but the digitized form of a
flora published online. Example: ‘e – Flora China’. This provides the
information and also functions as an identification tool.
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5.
Botanical gardens
Botanical
gardens are institutions holding
documented collections of living plants for the purpose of scientific research,
conservation, display and education. In 2018, BGCI updated the criteria that
define a botanic garden to have a greater emphasis on conserving rare and
threatened plants, compliance with international policies and sustainability
and ethical initiatives.
Gardens and the cultivation of plants have been around for
thousands of years with the first examples dating to around 3,000 years ago in
ancient Egypt and Mesopotamia.
For the purpose of science and
education the first garden was maintained by Theophrastus in
his public lecture hall at Athens.
First
modern botanical garden was established by Luca Ghini (1490-1556)
a professor of Botany at Pisa, Italy in 1544.
Botanical garden contains special plant collections
such as cacti, succulent, green house, shade house, tropical, alpine and exotic
plants. Worldwide there are about 1800 botanical gardens and arboreta.
Role of Botanical
Garden: Botanical Gardens play the following
important roles.
1. Gardens
with aesthetic value which attract a large number of visitors. For example, the
Great Banyan Tree (Ficus benghalensis) in the
Indian Botanical Garden at Kolkata.
2. Gardens
have a wide range of species and supply taxonomic material for botanical
research.
3. Garden
is used for self-instruction
or demonstration purposes.
4. It
can integrate information of diverse fields like Anatomy, Embryology, Phytochemistry,
Cytology, Physiology and Ecology.
5. Act
as a conservation
centre for diversity, rare and endangered species.
6. It
offers annual list of available species and a free exchange of seeds.
7. Botanical
garden gives information about method of propagation, sale of plant material to
the general public.
Importance:
1.
Botanic Gardens also play a very important role in
maintaining germ-plasm bank of different plants and act as a depository of
‘extinct’ and ‘endangered’ plants.
2.
Botanic Gardens play an important role in the ex
situ conservation of plant species.
Royal Botanic garden, Kew- England: Royal
Botanic garden Kew- England is a non- departmental public body in the United
Kingdom. It is the largest botanical garden in the world, established in 1760,
but officially opened in the year 1841.
Botanic Gardens of India:
1. Indian Botanic Garden,
Sibpur, Kolkata (1787).
2. Lloyd Botanic Garden,
Darjeeling, West Bengal (1878).
3. National Botanic Garden,
Lucknow (1946).
4. The Mysore State Botanic
Garden, Bangalore, Karnataka (1856).
5. Garden of the Forest
Research Institute, Dehra Doon (1934).
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6.
International Code of Botanical Nomenclature (ICBN)
Assigning name for a plant is known as Nomenclature. This
is based on the rules and recommendations of the International Code of
Botanical Nomenclature. ICBN deals with the names of existing (living) and
extinct (fossil) organisms.
The elementary rule of naming of plants was first proposed by Linnaeus in
1737 and 1751 in his Philosophia Botanica. In 1813 a detailed set
of rules regarding plant nomenclature was given by A.P. de Candolle in
his famous work “Theorie elementaire de la botanique”.
Then the present ICBN was evolved by following the same rules
of Linnaeus, A.P. de Candolle and his son Alphonse de
Candolle.
ICBN due to specific reasons and in order to separate plant kingdom from
other organisms, is redesignated as ICN. The International Botanical
Congress held in Melbourne in July 2011 brought this change. The ICN stands for
International Code of Nomenclature for Algae, Fungi and Plants
ICN Principles
International
Code of Nomenclature is based on the following six principles
1. Botanical nomenclature is independent of
zoological and bacteriological nomenclature.
2. Application of names of taxonomic group is
determined by means of nomenclatural types.
3. Nomenclature of a taxonomic group is based on
priority of publication.
4. Each taxonomic group with a particular
circumscription, position and rank can bear only one correct name, the earliest
that is in accordance with the rules except in specified cases.
5. Scientific names of taxonomic groups are treated
as Latin regardless of their derivation.
6. The rules of nomenclature are retroactive unless
expressly limited.
Codes of
Nomenclature
ICN has formulated a set of rules and recommendations
dealing with the botanical name of plants. International Botanical Congress is
held at different places every six years. Proposals for nomenclatural changes
and changes in rules are discussed and implemented. Changes are published in
their website.
18th International Botanical Congress held in 2011at
Melbourne, Australia made the following major changes.
1. The code now permits electronic publication of
names of new taxa.
2. Latin diagnosis or description is not mandatory
and permits the use of English or Latin for the publication of a new name
(Art-39).
3. “One fungus, one name” and “one fossil one name”
are important changes, the concept of anamorph and telomorph (for fungi) and
morphotaxa (for fossils) have been eliminated. (Previously, sexual and asexual
stages of the fungus/ fossils were provided with different names).
Anamorph – Asexual reproductive stage
of fungus.
Telomorph – Sexual reproductive stage
of fungus.
4. As an
experiment with “registration of names” new fungal descriptions require the use
of an identifier from a “recognized repository”. There are two recognized
repositories Index fungorum and Myco
Bank.
19th
International Botanical Congress was held in Shenzhen in China in 2017. Changes
accepted by International Botanical Congress are yet to be published.
Vernacular names
(Common names)
Vernacular names are known as common names. They are very often descriptive and poetic references to plants.
Common name refer to more than one plant or many plants may have same common
name. These names are regional or local and are not universal. Example: Albizia amara . L belongs to Mimosaceae is called as Usilai in South Tamilnadu and Thurinji in North Tamilnadu.
Each and every taxon as per the ICN (species, genus, family
etc) can have only one correct scientific name. Scientific name of a species is
always a binomial. These names are universally applied. Example: Oryza sativa L. is the scientific name
of paddy.
Polynomial
Polynomial is a descriptive phrase of a plant. Example: Ranunculus
calycibus retroflexis pedunculis falcatis caule erecto folius compositis. It
means butter cup with reflexed
sepals, curved flower stalks, erect stem and compound leaves. Polynomial system
did not hold good as it was cumbersome to remember and use. Polynomial system
of naming a plant is replaced by a binomial system by Linnaeus.
Binomial
Binomial nomenclature was first introduced by Gaspard Bauhin and it was implemented
by Carolus Linnaeus. Scientific name
of a species consists of two words and according to binomial nomenclature, the
first one is called genus name and
second one is specific epithet. Example: Mangifera
indica. Mangifera is
a genus name and indica is specific epithet. This system is in
vogue even now.
Author citation
This refers to valid name of the taxa accompanied by the
author’s name who published the name validly. Example: Solanum nigrum L. There are two types of author citation.
Single author: When a single author proposed
a valid name, the name of the author alone is accompanied by his abbreviated
name. Example: Pithecellobium
cinereum Benth.
Multiple authors: When two or more authors
are associated with a valid publication of name, their names should be noted
with the help of Latin word et or
&.
Example: Delphinium
viscosum Hook. f. et Thomson.
Standard form of
author’s abbreviations has to be followed.
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7.
Application of Plant systematics
Plant systematic has great importance for the study
of botany:
1. It is used to describe different species. The description of each
new species is preserved. It is used for comparison.
2. Plant systematic is used to name different plants. It sets rule for
nomenclature. ,This nomenclature has eliminated the confusion among
different botanists. Now knowledge of plants can be shared between botanists of
different countries without problem of language and culture.
3. Plant systematic develops evolutionary relationship among the different
groups of plants. It gives evolutionary trends among the plants.
4. Plant systematic provides basis kw the comparison of morphological,
anatomical and cytological structures among different structures.
5. Plant systematic also provides basis of genetics. Genetic analysis are
performed on the basis of systematic,
6. Plant systematic has great importance in agriculture and herbal
medicines. It provides us economic importance of different plants.
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8.
Typification (or)Type concept
Typification (Art.
7-9) A nomenclatural type (typus) is that element to which the name of a taxon is permanently
attached, whether as the correct name or as a synonym.
ICN’s second
principle states that a specimen must be associated with the scientific name
known as nomenclatural type. A nomenclatural type
is either a specimen or may be an illustration. Example: Herbarium
sheet for vascular plants.
There are different nomenclatural types.
a.
Holotype : A specimen or illustration originally
cited by the author in protologue. It is a definitive reference source for
identity. Citation of holotype and submission of it is one of the criteria for
valid publication of a botanical name.
b. Isotype: Duplicate
specimen of the holotype collected from same population by same
person on same date with same field number. They are the reliable duplicates of
holotype and may be distributed to various herbaria of various regions.
c.
Lectotype: Specimen selected from original
material serves as a type, when no holotype was designated at the time of
publications or if holotype is missing or destroyed.
d. Syntype: When more than
one specimen cited by the author in the protologue without
designating holotype.
e.
Neotype: Specimen derived from non-original collection
selected as the type, when original specimen is missing or destroyed.
f.
Paratype: Specimen cited in the protologue is
other than holotype, isotype or syntype.
g. Epitype: Specimen or illustration
serves as an interpretive type, when holotype, neotype or lectotype
is ambiguous.
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9. Phytochemisty/ Plant
Chemotaxonomy relation in taxanomy
Plant
Chemotaxonomy is one of the more fashionable and rapidly extending areas of
plant taxonomy that seeks to utilize chemical information to improve
classification of plants.
The
potential importance of chemical evidence in taxonomy was suggested by a number
of early taxonomists, i.e. Decandolle, Hoffman, Hallier and Molisch .
Chemical characters used in
Taxonomy
The chemical characteristics of plants can be categorized
as:
1. Starch, raphides, cystoliths, silica etc
2. Secondary metabolites, such as alkaloids,
flavonoids, terpenoids etc
3. Protein analyses
1.
Starch: Starch are the commonest
chemical substances which can be easily identified.
For examples:
· Acentric starch =
Solanaceae (Solanum tuberosum)
· Metacentric
(simple) starch = Fabaceae (Cicer arietinum, Pisum sativum)
· Metacentric
(compound) starch – Poaceae (Oryza sativa, Triticum aestivum)
2.
Raphides: They are calcium
oxalate. The granules of calcium oxalates may occur singly or in groups. After
Sectioning they can be observed under microscope. Raphides are not common in
all families, rather in a limited number, say for examples, they are found
around 35 angiosperm families, including Araceae, Palmae, Orchidaceae,
Typhaceae, Rubiaceae, Vitaceae. No raphide is found in the primitive families
of monocots.
3.
Cystolith: These are the
granules of Calcium carbonate which are found in leaf below the epidermis. Some
cells of hypodermis become larger where the granules of CaCO3 are found (look
like a bunch of grapes). Cystoliths are found in the families Acanthaceae,
Moraceae etc. The genus Ficus under Moraceae is very distinct by presence of
Cystolith.
4.
Silica: They are produced
through different metabolic processes. They are somehow significant to
characterize different families, for example, Conical shapes of cystolith is a
characteristic of the family Cyperaceae, while dumb-bell or saddle shapes
silica are found in Bambusoideae subfamily of Poaceae. Different palms can be
distinguished based on different shapes of silica.
COMPOUNDS USEFUL IN PLANT TAXONOMY
Although in theory all the
chemical constituents of a plant are potentially valuable to a taxonomists, in
practice, some sorts of molecules are far more valuable than others.
Apart from inorganic compounds (which are of little
use relatively), three broad categories of compounds are recognized.
These are:
i. Primary metabolites
ii. Secondary
metabolites
iii. Semantides
i. Primary metabolites
Primary metabolites are parts
of vital metabolic pathways, and most of them are universal occurrence, or at
least occur in a very wide range of plants.
Aconitic acids (first isolated
from Aconitum) and Citric acid (from Curs) are present in
all aerobic organisms. Presence or absence of such compounds have not much
taxonomic value. However, in some cases the quantities of such metabolites vary
considerably between taxa, can be taxonomically useful.
ii.
Secondary Metabolites
The chemical substances which
have been found very useful in taxonomy are secondary metabolites. Secondary
metabolites (secondary plant products) perform non-vital (or at least non-
universally vital) functions, and are less widespread in plants. The restricted
occurrence of these metabolites among plants renders them valuable as taxonomic
information.
Secondary plant products are
largely waste substances, food stores, pigments, poisons, scents, structural
units or water repellents, etc.
The most well-known groups of
secondary metabolites are phenolic compounds, alkaloids, glucosinolates, amino
acids, terpenoids, oils and waxes, and carbohydrates.
Ex. Alkaloids
Alkaloids are nitrogen based
chemical compounds which are found in different plant groups. Some alkaloids
are very specific, for instance –
· Morphine – only in Papaver somniferum (Papaveraceae) and this
alkaloid is not found in any other species. That means Papaver somniferum can easily be identified by
presence of morphine.
· Serpentine – Rauwolfia serpentina.
· Aconitine – Aconitum napellus (Ranunculaceae) .
iii.Semantides
Semantides are
information-carrying molecules. Semantides provide taxonomic data not on the
basis of presence or absence, but in terms of sequences, ratios or
percentages,.
Semantides are of three types, viz.,
· Primary semantide
– DNA
· Secondary
semantide- RNA
· Tertiary
semantides – Proteins
Protein taxonomy are divisible into three main headings: a)
electrophoresis, b) Serology, c) amino acid sequencing.
*****
10. Molecular taxonomy (molecular systematics / molecular
phylogenetics)
Molecular
Taxonomy is the branch of phylogeny that analyses hereditary molecular
differences, mainly in DNA sequences, to gain information and to establish
genetic relationship between the members of different taxonomic categories. The
advent of DNA cloning and sequencing methods have contributed immensely to the
development of molecular taxonomy and population genetics over the years.
These modern methods have revolutionised the field of molecular taxonomy and
population genetics with improved analytical power and precision.
Molecular Markers
Allozyme
electrophoresis is a method which can identify genetic
variation at the level of enzymes
that are directly encoded by DNA.
1.Mitochondrial DNA markers are
non- nuclear DNA located within organelles in the
cytoplasm called mitochondria. The entire genome undergoes transcription as one
single unit. They are not subjected to recombination and thus they are
homologous markers.
2.Microsatellite is a
simple DNA sequence which is repeated several times across various
points in the DNA of an organism. These (usually 2-5) repeats are highly
variable and these loci can be used as markers. (Example: TGTGTG, in which two
base pairs repeat, the region are termed tandem
repeat.)
3.Single nucleotide polymorphisms arise
due to single nucleotide substitutions (transitions/transversions)
or single nucleotide insertions/deletions. SNPs are the most abundant
polymorphisms in the genome (coding and non-coding) of any organism. These
single nucleotide variants can be detected using PCR, microchip arrays or
fluorescence technology.
4. DNA microarray or DNA chip consists
of small glass microscope slides, silicon chip
or nylon membranes with many immobilized DNA fragments arranged in a standard
pattern. A DNA microarray can be utilized as a medium for matching a reporter
probe of known sequence against the DNA isolated from the target sample which
is of unknown origin. Species-specific DNA sequences could be incorporated to a
DNA microarray and this could be used for identification purposes.
5. Arbitrary markers are
sometimes used to target a segment of DNA of unknown function.
The widely used methods of amplifying unknown regions are RAPD and AFLP DNA.
6. Specific Nuclear DNA markers: Variable
Number of Tandem Repeat is a segment of
DNA that is repeated tens or even hundreds to thousands of times in nuclear
genome. They repeat in tandem; vary in number in different loci and differently
in individuals. There are two main classes of repetitive and highly polymorphic
DNA viz. minisatellite DNA
referring to genetic loci with repeats of length 9-65 bp and microsatellite DNA
with repeats of 2-8 bp (1-6) long. Microsatellites are much more numerous in
the genome of vertebrates than minisatellites.
The results of a
molecular phylogenetic analysis are expressed in the form of a tree called phylogenetic tree. Different molecular markers like allozymes, mitochondrial DNA,
micro satellites, RFLP (Restriction Fragment Length Polymorphism), RAPD (Random
amplified polymorphic DNA), AFLPs (Amplified Fragment Length Polymorphism),
single nucleotide polymorphism- SNP, microchips or arrays are used in analysis.
Uses
of molecular taxonomy
1. Molecular taxonomy helps in establishing
the relationship of different plant groups at DNA level.
2. It
unlocks the treasure chest of information on evolutionary history of organisms.
3. DNA taxonomy plays a vital role in phytogeography,
which ultimately helps in genome mapping and biodiversity conservation.
4. DNA- based molecular markers used for designing DNA
based molecular probes, have also been developed under the branch of molecular
systematics.
RFLP
(Restriction Fragment Length Polymorphism)
RFLPs is a molecular method of genetic analysis that allows identification of
taxa based on unique patterns of restriction sites in specific regions of DNA.
It refers to differences between taxa in restriction sites and therefore the
lengths of fragments of DNA following cleavage with restriction enzymes.
Amplified
Fragment Length Polymorphism (AFLP)
This method is similar to that of identifying
RFLPs in that a restriction enzyme is used to cut DNA into numerous smaller
pieces, each of which terminates in a characteristic nucleotide sequence due to
the action of restriction enzymes.
AFLP is
largely used for population genetics
studies, but has been used in studies of closely related species and even in
some cases, for higher level cladistic analysis.
Random
Amplified Polymorphic DNA (RAPD)
It is a method to identify genetic markers
using a randomly synthesized primer that will anneal (recombine (DNA) in the
double stranded form) to complementary regions located in various locations of
isolated DNA. If another complementary site is present on the opposing DNA
strand at a distance that is not too great (within the limits of PCR) then the
reaction will amplify this region of DNA.
RAPDs like
microsatellites may often be used for genetic studies within species but may
also be successfully employed in phylogenetic studies to address relationships
within a species or between closely related species. However RAPD analysis has
the major disadvantage that results are difficult to replicate and in that the
homology of similar bands in different taxa may be nuclear.
Significance
of Molecular Taxonomy
1. It helps to identify a very large number of
species of plants and animals by the use of conserved molecular sequences.
2. Using DNA data
evolutionary patterns of biodiversity are now investigated.
3. DNA taxonomy plays
a vital role in phytogeography, which ultimately helps in genome mapping and
biodiversity conservation.
4. DNA-
based molecular markers used for designing DNA based molecular probes, have
also been developed under the branch of molecular systematics.
U
SRIDAR
DEPT.
OF BOTANY
VC-KTDM
