Molecular Taxonomy Introduction
With the rapidly growing knowledge of genetics and molecular biology, phylogeny has received a new motivation. Phylogeny provides a new source of evidence about the course of evolution. While comparing total genes of two different species, if the genetic differences between them are minor, they are liable to be closely related. In other word, the degree of genetic difference indicates the closeness of that relationship.
There may be huge practical and theoretical problems as animals have so many genes. Moreover the presence of particular genes does not define their effects. The action of genes depends upon the presence or absence of many other factos. Also a small change in genes can make a big difference in animals. For example, Humans share about 99% genes with Chimpanzees and it is that remaining 1% genes that make us Humans.
The rate of genetic change and the rate of species change are not same. Both rate of genetic change and the rate of species change have not remained constant through the evolution. During the evolution, when there is a change in a gene, its immediate product (molecules) changes slowly. The comparison of the amount of change in that gene product will reveal the familiarity of the relationship of different groups of animals. Therefore, molecules can be used as morphological characters to study the evolutionary history.
For example, compare a particular gene within a range of populations like shrimps, insects and spiders. This comparison must first the show that different insect populations resemble each other more closely than spiders or shrimps. Then secondly it must show which tow of the three groups are most closely related. During comparison, molecular characters can be replaced for morphological characters to evaluate the relatedness of animals.
Molecules used in molecular taxonomy
Initially molecular taxonomy studies were conducted using proteins which are the products of gene action. But currently work is concentrated much on DNA and the genes themselves. The following are the molecules used in the molecular taxonomical studies.
Ribosomal DNA (rDNA): The genes coding for small subunit of 18S ribosomal DNA (rDNA) are used in molecular taxonomy studies because,
- Mutations are unlikely to survive natural selection and these genes have very less mutations.
- These genes are highly conserved and have changed very slowly during evolution.
- They have important structural role.
The rDNA can therefore provide important clues regarding changes that occurred very early in evolution such as the segregation of classes within a phylum or origin of the new phyla.
Genes regulating early development: Genes acting early in development guide the fate of cells and thus may be very informative. Comparison between phyla is based on the molecular evidences obtained using ribosomal genes. The information about the divergence which has occurred during evolution can be obtained from these genes.
Using more than one gene and testing various aspects of evolutionary change may avoid some of the disadvantages which occur in using ribosomal genes (rDNA).
Mitochondrial DNA (mtDNA): The genes situated in the mitochondria are different from nuclear genes and these genes have useful sources of information. It is not the gene content of the mitochondria that is used but the order of genes round the chromosomal ring. In most animals, the contribution of sperm to the zygote is zero and therefore mitochondrial inheritance is confined only to the females. This uniparental dependence further simplifies the use of mtDNA.
Mitochondrial DNA changes comparatively fast in evolution and it is useful to determine changes that have occurred less than 15 million years ago. When the whole genome is sequenced, mitochondrial DNA gives the information about ancient changes.
Methods of obtaining molecular information
The differences between proteins can be revealed and estimated using gel electrophoresis. But the techniques which are applied directly to DNA are more preferred.
DNA hybridization: DNA hybridization is based on the principle that, upon heating the bonds between corresponding nucleotides of DNA are broken and consequently double stranded DNA dissociates. These disassociated strands recombine when cooled and bonds are formed only at corresponding sites. When single strands of DNA from related species are put together they form hybrids. When such hybrid pairs are heated, they get separated at a temperature much lower than the one required to separate original DNA pair. This is because of the formation of less number of bonds. This temperature difference is used as a measure of genetic similarity between the two species.
Restricted site analysis: Restriction analysis is based on the working of restriction enzymes. Restriction enzymes perfectly cut DNA into fragments at expected sites. Fragments from different sources are compared to obtain information about a small part of the total molecule.
Sequencing of nucleotides: The sequencing of nucleotides allows the identification of each nucleotide in whole sequence of a DNA molecule. This comprehensive process has been made easier by the polymerase chain reaction (PCR), which amplifies a small quantity of material for rapid analysis and automated sequencing machine. PCR technique opened new avenues in exploration of molecular information.
Processing of the molecular information
Molecular evidence gives a large number of well-defined characters. A given nucleotide at a given site on the DNA molecule is known as a character. Traditional methods of evaluating characters are not applicable to study molecular differences but phenetic analysis can be easily applied.
During the process of evolution, if molecular change increases at a constant rate then the amount of change is the measure of evolutionary distance. Though, genes do not always change at a constant rate.
Reliability of molecular taxonomy
Day by day the number of animals being studied with the help of molecular taxonomy is increasing and consequently the confidence in molecular taxonomy is also growing. Though molecular taxonomy is reliable, it has few disadvantages over advantages.
- As the nature and precise position of the unit can be defined exactly, the data is equivalent.
- The size of the data used in molecular taxonomy studies is enormous.
- The analysis of the cladograms is done using statistical methods.
- In case the molecule is unchanged (Example, genes coding for ribosomal RNA), the relationships can be traced far back in time.
- Non-heritable variations are avoided in molecular taxonomy studies.
- In cladistics, it is assumed that change in a gene molecule will depend only on the mutation rate and the time elapsed. In other words, it is assumed that an unvarying molecular clock is ticking at a regular rate. But, the clock is known to be variable in certain conditions and the whole idea of functionally neutral changes in genes is debatable.
- There is no record of past changes in characters. This is a very serious disadvantage as there are only four possible nucleotides for any given site in DNA molecule. There might have been changes from one nucleotide to another and back again. Such multiple hits cannot be analyzed.
- There is no familiar intermediate condition between characters and no primitive condition for a given DNA site can be recognized.
- The tracing of functional correlates of character is very rare.
- It is very difficult indeed to root a tree derived from molecules; As sequence similarity is the only guide it is difficult to root a tree derived from molecules. Moreover the likelihood of convergence is usually impossible.
The study of antigen-antibody reaction is called serology. The substance capable of stimulating the formation of an antibody is antigen. A specific protein molecule produced by plasma cell in the immune system is antibody. The antibodies combine chemically with specific antigen and this combination elevates an immune response. The application of serology in solving taxonomic problems is called serotaxonomy.
Nuttal was the first biologist to compare immunochemical specificity of serum proteins for systematic purposes in 1901. Later in 1910, Dunbar showed theta proteins from pollen, seed and leaves of rice were serologically distinct. In 1914, Gholke established serology school in Germany and later Germany became the center of serological studies.
Process of Serotaxonomy
The process of serotaxonomy involves the following steps:
- The protein extract of the plant origin i.e. the antigen is extracted.
- The antigen is injected into the blood stream of an experimental animal to form antibodies.
- The experimental animal produces specific antibody in response to the antigen.
- The serum with antibodies is called antiserum. Antiserum is made to react in vitro with antigenic protein as well as proteins of other taxa, whose affinities are to be determined.
- The amount of precipitation shows the degree of homology.
For example, to know the closeness of the taxon A with B, C, D, E
The proteins from A are extracted and are injected into the experimental animal rabbit or mice. The experimental animal in return produces antibodies. These antibodies are extracted from the blood of the experimental animal in the form of antiserum.
- When this antiserum is allowed to react with the original protein extract from A, complete coagulation takes place.
- When this antiserum is allowed to react with the protein extracts from other taxa B, C, D, E the degree of coagulation varies.
- The degrees of coagulation are compared to know the closeness of the taxa. More the degree of coagulation more is the closeness.
Importance of serotaxonomy
There are several instances where the serological data has been used to classify angiosperms. Some of them are mentioned below:
- In 1983, Fairbrothers used serological data in classification of orders and assignment of families in Apiales, Fagales, Magnoliales, Juglandales, Rubiales, Ranunculales etc
- Again in 1959, Fairbrothers and Jhonson separated six species of Bromus on the basis of the serological data.
- On the basis of the serotaxonomic studies Fairbrothers and Jhonson showed that genera Magnolia and Michelia show closest affinity within Magnoliaceae
- Simon in 1971 demonstrated close relationship between Nymphaeaceae and nelumbonaceae based on serological data.
- Klos applied serotaxonomic data in the classification of Leguminosae.
- What is molecular taxonomy?
- What are the molecules used in Molecular taxonomic studies?
- Write about the genes which regulate early development.
- What is DNA hybridization?
- How is the molecular information processed?
- Enumerate the advantages and disadvantages of Molecular taxonomy?
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