Molecular Taxonomy | Zoology Optional Notes for UPSC PDF Download

Organisms

Organisms are characterized by unique biological attributes which enhance their fitness and survival to a particular environment. The driving force for enhanced survival and fitness is the genetic variation inherent in an individual as well as in a population. The information regarding genetic diversity and variation has wide application in research on evolution, conservation and management of natural populations.

Molecular Taxonomy and Population Genetics

The advent of DNA cloning and sequencing methods have contributed immensely to the development of molecular taxonomy and population genetics over the last 2 decades. These modern methods have revolutionized the field of molecular taxonomy and population genetics with improved analytical power and precision.

Molecular Markers

Molecular markers can be characterized as Type I and Type II markers; Type I markers are associated with genes of known function and type II markers are associated with genes of unknown function. Allozyme markers are type I markers as the proteins they encode are associated with some functions. Microsatellites and other neutral markers are type II markers unless they are associated with genes of some known function.

Allozyme

Allozyme electrophoresis is a method which can identify genetic variation at the level of enzymes that are directly encoded by DNA. Allozymes are codominant markers having been expressed in a heterozygous individual in a Mendelian way. Allozyme analysis provides data on single locus genetic variation which can answer many questions about fish and fish populations.

• Allozymes can be detected through electrophoresis in an acrylamide or cellulose acetate gel.
• Allozymes are one of the most studied forms of molecular variation due to their simplicity, low cost, and requirement of little specialized equipment.
• Allozyme analysis has been widespread in fisheries mainly in fish systematics, population structure, conservation genetics, mixed stock fishery analysis, and forensic analysis.

Mitochondrial DNA Markers

Mitochondrial DNA is non-nuclear DNA in the cell located within organelles in the cytoplasm called mitochondria. Mitochondrial DNA is maternally inherited with a haploid genome. It is physically separate from the rest of the cell’s DNA and so it is relatively easy to isolate from any tissue or blood sample. Mitochondrial DNA markers are widely used in fish taxonomy, biology, and population genetics.

Arbitrary Nuclear DNA Markers

Arbitrary markers are used when targeting a segment of DNA of unknown function. RAPD (Random Amplified Polymorphic DNA) and AFLP (Amplified Fragment Length Polymorphism) DNA are widely used methods of amplifying unknown regions. RAPD uses an arbitrary primer which can amplify anonymous loci. AFLP markers combine the benefits of both RFLP and RAPD.

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 the nuclear genome of eukaryotes. They repeat in tandem, vary in number in different loci and differently in individuals. Minisatellites and microsatellites are widely used in population genetics of fishes and aquatic invertebrates.

Microsatellites

Microsatellites are simple DNA sequences that are repeated several times across various points in the DNA of an organism. They are highly variable, non-coding, and selectively neutral. Microsatellites are codominant markers which are inherited in a Mendelian fashion and are highly evolving. They are used in fisheries and aquaculture for various purposes including phylogenetics, population genetic structure, biodiversity conservation, and forensic identification.

Applications of Molecular Markers in Fisheries

• Inter-specific and intra-specific variations
• Phylogenetic and phylogeographic studies
• Structure of populations: between and within populations
• Genetic tagging/marking
• Forensic investigation
• Studying the trophic relationships
• Analysis of ancient DNA
• Applications in aquaculture

Molecular markers have a wide range of applications in fisheries and aquaculture. Their use has revolutionized the field of fish genetics and has contributed to various research areas including taxonomy, population genetics, conservation, and aquaculture. It is important to carefully choose the appropriate marker type for each specific application to maximize the quality of results.