7.4 Molecular techniques as Taxonomic tools

In order to categorize species based on genetic information and elucidate evolutionary relationships that may not be evident from morphology alone, scientists now rely heavily on molecular techniques in taxonomy. These methods, which frequently offer more accuracy and insight than conventional morphological methods, use DNA, RNA, and protein sequence analysis to identify, categorize, and investigate relationships among species.

Key Molecular Techniques in Taxonomy

1. DNA Sequencing
   • The exact arrangement of nucleotides in a DNA molecule is ascertained through DNA sequencing. This offers a genetic blueprint that can be utilized for molecular species comparison.By comparing the DNA sequences of particular genes or genomes across species, species connections are frequently clarified and new species are frequently discovered.
   • DNA sequencing has revolutionised the field of taxonomy.  Morphological qualities, which can be unclear or inconsistent, particularly in species with few distinguishable physical characters, were a major problem in  traditional taxonomy. By examining genetic data, DNA sequencing gets over these restrictions and offers a more accurate and impartial classification.

“DNA sequencing” by DYCLDYCL, creativecommons.org via Wikimedia Commons is licensed under CC BY-SA 4.0

Role of DNA Sequencing in Taxonomy

• Identification and Categorization: DNA sequences function as distinct molecular “barcodes” that allow for the identification of species. While ribosomal RNA (rRNA) genes are frequently employed for plants and microorganisms, mitochondrial genes, such as cytochrome c oxidase I (COI), are frequently used for animal DNA barcoding.

• Phylogenetic Analysis: The construction of evolutionary links between species is aided by DNA sequencing.
  Taxonomists can track lineage divergence and comprehend evolutionary history by comparing DNA sequences.
• Resolving Cryptic Species: Species that have the same morphology but differ genetically are known as cryptic species. These subtle variations can be found by DNA sequencing, which improves categorization accuracy.
• Microbial Taxonomy: Microorganisms cannot be adequately classified using morphological approaches. A fundamental component of microbial taxonomy is DNA sequencing, particularly of 16S rRNA genes.
• Classification Revision: Sequencing can support or contradict current taxonomic classifications. Genetic information can be used to remedy morphologically based misclassifications.

2. DNA Barcoding

• • DNA barcoding is a contemporary method for classifying and identifying species. It has transformed taxonomy by offering a quick, accurate, and economical way to differentiate between species. DNA barcoding utilizes short standardized DNA sequences from particular genomic areas,  for classifying and identifying species.

Core Principles of DNA Barcoding

• • Standardized DNA Regions: A  shortgenomic sequence is selected to serve as the “barcode.”
    The mitochondrial DNA-derived cytochrome c oxidase I (COI) gene is extensively utilized in mammals.
    Chloroplast DNA contains genes like matK and rbcL that are frequently found in plants.
    The internal transcribed spacer (ITS) region is typical for fungus.
  • Species-Specific Variability: To guarantee precise identification, the selected area must differ greatly between species while remaining conserved within a species.
  • Reference Databases: In order to compare species, DNA barcoding uses databases like GenBank and BOLD (Barcode of Life Data System), which contain reference sequences.

“DNA Barcoding” by LarissaFruehe, creativecommons.org via Wikimedia Commons is licensed under CC BY-SA 4.0

Applications of DNA Barcoding

Species Identification: By matching barcodes with reference databases, it can quickly identify recognized species.
Helps detect mislabeled or misidentified organisms.
The discovery of new species  :reveals cryptic species that differ genetically yet have the same morphology.
Biodiversity Monitoring: Using eDNA (environmental DNA) barcoding, it is possible to identify species in environmental samples like soil, water, or air.
Conservation biology: Supports population genetic diversity monitoring and endangered species identification.

Food safety and agriculture: identifies pollutants, pests, or invasive species in agricultural products. Avoids fraud and confirms the legitimacy of food goods.
Biosecurity and Forensics: Applied in wildlife forensics to stop the illicit wildlife trade. Detects harmful or invasive species during biosecurity operations.

3. Polymerase Chain Reaction (PCR) 

Modern taxonomy relies heavily on the Polymerase Chain Reaction (PCR), a molecular biology technology that amplifies particular DNA sequences. PCR has greatly improved the accuracy and efficiency of species identification, categorization, and phylogenetic studies by making it possible to analyze minuscule amounts of DNA. Its ability to amplify specific DNA regions has broadened the scope of taxonomic studies, from ancient DNA analysis to environmental biodiversity monitoring.

PCR makes it easier to study species that are challenging to sample, including ancient specimens or environmental DNA (eDNA), by amplifying particular areas of DNA, even from tiny or deteriorated samples.Combining PCR with sequencing is crucial for characterizing microbial communities, particularly those that are cannot be cultured in  laboratory .

4.Restriction Fragment Length Polymorphism (RFLP)

By detecting variations in the lengths of DNA fragments generated by restriction enzymes, a molecular approach known as restriction fragment length polymorphism (RFLP) examines variations in DNA sequences.Variations in the DNA sequence can cause changes in the pattern of fragment lengths,after cut by restriction enzymes.In taxonomy, RFLP has been extensively utilized for phylogenetic analysis, genetic diversity research, and species identification.

“Gel Electrophoresis in DNA Fingerprinting” by Jennifer 0328,creativecommons.org, via Wikimedia Commons is licensed under CC BY-SA 4.0

Limitations of Molecular Techniques in Taxonomy

• Cost and Technical Requirements: Certain molecular techniques can be expensive and requires specific equipments
• Data Interpretation: In the absence of supplementary morphological or ecological information, molecular data alone can occasionally be deceptive.
• Complexity of Genomic Data: Accurate analysis and interpretation of large datasets necessitate the use of computational tools and bioinformatics knowledge.By offering reliable ways to recognize, categorize, and investigate the relationships between species, molecular tools have completely changed taxonomy and greatly improved our knowledge of biodiversity and evolutionary history.