Tools of Systematic Botany| Taxonomy

In this article we will discuss about the Tools of Systematic Botany:- 1. Geographic Information System 2. Molecular Techniques.

1. Geographic Information System (GIS):

The latest technique used as a tool in Biosystematics is Remote sensing and the use of computer.

Remote sensing is carried out by satellites to get an idea of the particular phytogeographical area. It was first used in 19th century by using camera. But now the technology is well developed and pictures are provided by the satellites.

Geographical information system gives the information about an area. Computer and software is required for interpreting results.

A Geographic Information System (GIS) captures, stores, analyzes, manages, and presents data, which is linked to a location. It includes mapping software and its application with remote sensing, land surveying, aerial photography mathematics, photogrammetry, geography, and tools that can be implemented with GIS Software.

GIS technology is used for scientific investigation, resource management archaeology, environment impact assessment cartography, criminology and topography etc. It is also used for calculating natural disaster.

GIS Software:

GIS can be assessed, transferred, overlaid, transformed, processed and displayed using various software. Many softwares are offered by several companies e.g., Bentley System, ESRI, Marifold system, Small world etc. offer an entire suite of tools.

Government and military departments often use custom software, open source products e.g., GRASS or uDig etc. Free tools exist of view GIS datasets, public access to geographic information dominated by online resource such as Google Earth and interactive Web mapping.

GIS is used for:

(a) Mapping of:

(i) Patterns:

i.e., Distribution of plants in an area that produces a definite pattern.

(ii) Features:

i.e., Mapping of individual features.

(iii) Quantities:

It means maps are prepared showing the frequency and abundance of the vegetation of the area. Information about the inner-relationship between the places could be calculated out of it.

Changes:

Mapping at different times of a particular place can also provide the data of changes occurring in the particular area. It helps in evaluating and taking measures of correction.

Mapping provides the type of plants in that particular area. Though it is aerial survey but when one knows about the plants in the area then one can also knew about the climate, the soil and irrigation etc. The environment of surrounding area may also be known easily.

Merits:

Mapping also provides the concentration of vegetation of the area, i.e., the density of vegetation which is observed by aerial survey e.g., distribution of plants, their canopy structure etc.

For GIS analysis first one should frame question in mind and select the data according to it. After selection of the data it is processed for analysis. Finally the results are in the form of mapping. The software used for the purpose should be flexible enough to allow the display of results in the best suited format.

GIS helps in investigation of an area and allow the taxonomists to improve management of the resources. GIS is not mapping but a way of getting better view of canopy, vegetation and other things from distant place. GIS creates maps from data gathered from Database, GIS not only can give information (mapping) about the area but even it can analyze the individual (plant or a human body).

Remote sensing involves the detection and measurement of the radiation of different wavelengths of light emitted or reflected from distinct objects, helping on their identification.

The process needs:

(a) Energy source,

(b) Transmission path,

(c) Target, and

(d) Satellite sensor.

Energy source here is the electromagnetic energy, which serves the medium for transmitting information from target to sensor (electromagnetic spectrum). Electromagnetic energy comes from extremely short wave lengths like cosmic gamma rays (<0.03 nanometer) to extremely long wavelength like radio and television wave (microwaves 3-300.0 cms).

Remote sensing systems are mainly of two types Active and Passive systems:

(a) Active system:

The system generates its own electromagnetic relation and measures the intensity of the return signal. Sensor provides its own illumination. Example of it is Synthetic Aperture Radar (SAR).

(b) Passive system:

The system consists of small sensors which can record electromagnetic radiation reflected or emitted from the earth’s surface. Passive visible and near infrared data are used in most of the GIS applications and in its classification of vegetation etc.

2. Molecular Techniques:

Molecular techniques as taxonomic tool is of very recent development. Rapid advancement in molecular biology of plants influenced taxonomists in this respect. The direct application of the molecular parameters as taxonomic feature is relatively less developed.

DNA profiles are most widely used in classification. Intra-specific variation can be detected easily. Other parameters used is molecular sequences. It offers the most unambiguous and reliable basis for phylogenetic as well as systematic consideration.

DNA Profile Making:

Eukaryotic genome has a variety of sequence types including various claims of repetitive and non-repetitive types. The methods which reveal specific DNA sequence distribution patterns are generally known as DNA profile methods. The important DNA profile methods are DFP (DNA finger printing) and MAAP (Multiple Arbitrary Amplican Profiling).

DNA Finger Printing:

DNA finger printing is a useful technique for genotype determination. It is possible to trace gene-flow amongst individual in the population to establish genetic relationship. Individual genotype can be identified at molecular level on the basis of an extremely high level of polymorphism in the sequence of its DNA. DNA finger printing adequately describes intra-population genotype distribution.

Nybom (1993) considered it difficult to analyse inter-population and interspecies levels of genetic variation. By using appropriate probes, finger printing has been employed to classify group of organisms as in same fungi by Meyer 1992, Bannane  Dandelions and Carnationetc.

MAAP:

Caetano-Anolles 1994 described Multiple Arbitrary Amplicon Profiling (MAAP) collectively for three versions, i.e., RAPD (Randomly Amplified Polymorphic DNA), Ap-PCR (Arbitrarily-primed PCR) and DAF (DNA Amplification Finger Printing) etc.

In these methods a single primer of arbitrary nucleotide sequence anneals to the genomic DNA at two different site on opposite strands and if these primer annealing sites are within an amplifiable distance of each other, discrete products are formed, the number of which depends on the genome size and the homology between primer at the template DNA sequences.

RAPD or Ap-PCR analysis have enabled the determination of phenetic relationship and extent of variability in Lycopersicum esculentum Adams and Demeke in 1993 described systematic relationship in Juniperus.

Genetic diversity and phylogeny in Azolla was studied by Coppenolle in 1993. Systematic or phylogentic studies in Stylosanthes by Kazan 1993, Lotus by Campos 1994 and Lens by Aboelwafe 1995 were also carried out.

Chloroplast DNA Profile:

Palmer (1985, 1987, 88) studied the chloroplast DNA as taxonomic or phylogenetic parameter. According to them the comparison of restriction site data in chloroplast. DNA’s has generally been applied to examine relationship among closely related species or genera. For example, in Family Asteraceae chloroplast DNA variation was examined in 57 genera belonging to 15 tribes.

The analysis suggested that 927 cleavages sites for 11 restriction enzyme tested suggested phylogenetic relationships. Doyle 1993 used chloroplast DNA profile in family Leguminosae. The data was found to be useful in classification at the genus and species levels but it was also useful at higher taxonomic levels as tribes and families.

In genus Astragalus within the tribe Galegeae the chloroplast DNA profiles were generated using specific genes such as rpo C₁ and rpo C₂ as probes by Sanderson and Liston in 1995. The results confirmed polyphyletic origin of Galegeae illustrating division within Galegea in general and Astragalus in particular.

Molecular Sequences for Phylogenetic and Systematic Analysis:

Primary sequences of nucleic acids and proteins are considered as a parameter for phylogenetic as well as systematic analysis. The use of protein and nucleic acid sequences in molecular taxonomy depends on sequence data. Nucleotide or/and amino acid sequences in a large number of organisms need to be determined.

The extent of variability in these sequences within a genus or a species needs to be determined before these can be as taxonomic parameters. The rate of evolutionary changes in sequences should be compared well with the level of divergence of the species concerned.

Mode of sequence evolution should be gradual and not adaptive. Only evolutionary changes which are qualitatively similar should be considered for a comparative study.

The genus encoding 5S RNA (5S DNA sequences) occur in thousands of copies with similar structure. Each unit of repetition consists of coding sequences which is 120 bp long and a spacer sequence of 100-700 bp long with several units arranged in tandem.

Repeat unit arrangement of 5S DNA sequences are considered to be a good parameter of phylogeny and systematics. Sastri (1992) has given by an overview of evolution in plant 5S DNA sequences. Playford 1992 studied the sequence in Acacia sp.

Phosphoenol pyruvate carboxylase sequences (PEP) is an important enzyme of metabolism especially of C4 plants. The amino acid sequence of PEP carboxylases are known-from 17 different Organisms.

Toh (1994) determined the molecular evolution in PEP carboxylases and predicted divergence time of the enzyme between monocots and dicots. Lower organisms (Bacteria, Cyanobacteria) can be easily separated from higher plants. Three distinct groups of the enzymes are identified on the basis of primary sequences of proteins.

Satellite DNA is a taxonomic marker. Lapitan (1992) identified many examples where satellites DNA is species-specific character, e g., satellite DNA is present in Solarium brevidens while absent in Solarium tuberosum. Satellite DNA in tomato wheat Barley and Rye etc. have also been found to be species-specific.

Chromosomal bands reflecting different heterochromatic regions also are proposed as good molecular parameters of the major molecular approaches. The PCR based technology shows maximum potential for phylogenetics and systematics taking into account the limitations of morphological marker DNA based molecular marker in conjunction with morphological and biochemical markers are serving as a better taxonomic tool.

DNA markers are devoid of environmental and developmental influences, unlimited in number to detect polymorphism, devoid of pleotropic and epiplastic tremendous discriminatory power, which is consistent under identical experi­mental conditions.

Recently such molecular markers are identified including hybridization based markers as RFLPs, Repeat elements, Microsatellites, Minisatellites, PCR based markers as Ap-PCR, MP-PCR, ISSR, STS, STMS, SCAR, DAF, AFLP etc.

DNA based molecular markers applied in various aspects on taxonomy to analyse genetic identity, genetic relatedness among population, geographic populations and species, Pedigree, phylogenetic structure at various macro and micro-levels, and differentiation among isolated species.