What is the origin and basis of Molecular Phylogeny?

The first practical approach of Molecular Phylogeny took place in the 18^th century by Lennaeus. He wanted to organize organisms into categories according to their physical characteristics, for example, phylum, class and order. Eventually, Lennaeus came up with a phylogeny which was described to be similar to the ‘tree of life’ developed by Darwin. However, a phylogeny showed the evolutionary relationships among the organisms.

Molecular Phylogeny can also be referred to Phylogenetic Systematics which is understood as the study of the relationships among different organisms whether being living or dead. The similarities or relationships among organisms, is believed to be based on their common ancestry. This understanding stems from the evolutionary theory. Phylogeny is that aspect of systematics that deals with the historical relationships among organisms by studying their genes. The best way Scientists have described the relationships among the organisms is through the construction of phylogenetic trees.

Phylogenetic trees are constructed by applying the sequencing of DNA and focuses on:

• DNA sequence alignment and acquiring the comparative data for tree construction
• Making a reconstructed tree using data collected
• Checking accuracy
• Allocating dates to branching points within the tree by the utilization of molecular clocks

Phylogenetic trees can take varying forms. Firstly, they can be rooted or unrooted. Rooted phylogenetic trees have distinctive nodes conforming to the most recent common ancestor of all individuals at the leaves of the tree. An unrooted tree demonstrates the connection of the leaf nodes without any hint of ancestral linkage. Both rooted and unrooted phylogenetic trees can be bifurcating (branches split into 2) or multifurcating (branches are split multiple times) and are either labelled or unlabelled. Labelled trees have explicit values allocated to its leaves, whereas unlabelled trees solely describe topology.

The following is a link to an interactive phylogenetic tree:

http://itol.embl.de/

The basis of Molecular Phylogeny is DNA sequencing. With the expansion of the knowledge of the structure of DNA, many applications of Molecular Phylogeny have been developed. Some are as follows:

1.      In the study of the epidemiology of AIDS  

2.      In the application of genetic fingerprinting      

3.      To determine a child’s paternity based on genetic testing

4.      To study human prehistory

Definitions of key terms and phrases:

1. Molecular Phylogeny: The study of evolutionary relationships among organisms using structures of molecules for example DNA and RNA.
2. Molecular systematics: An alternative form for defining molecular phylogeny.
3. Haplotype: The particular sequence of bases found in an organism.
4. Phylogenetic tree: A diagrammatic tree which shows the evolutionary relationships among organisms based on genetic and/or physical characteristics.
5. Dendrogram: a comprehensive term used to describe the illustration of phylogenetic trees.
6. DNA Sequencing: the procedure applied to obtain the ordered arrangement of nucleotides (adenine, guanine, cytosine & thymine) in DNA molecules.
7. Polymerase Chain Reaction (PCR): Amplification of DNA segments using denaturation cycles, heating and cooling of DNA and DNA synthesis that is directed by DNA polymerase.
8. Restriction fragment length polymorphism (RFLPs): Changes in  fragments of DNA due to the action of restriction endonucleases.
9. Microsatellites: Tandem repeats of sequences of DNA bases or nucleotides.
10. Mitochondrial DNA: Refers to the DNA found in the mitochondria.
11. Multiallelic genes: Multiple genes which affects the same or different hereditary characteristics.

Limitations of phylogenetic analyses:

• Horizontal gene transfer occurs when an organism’s genetic material is integrated into another’s who is not the offspring.
• Hybridization in this context refers to the resultant offspring of organisms that are not of the same taxa.
• Conserved sequences are orthologous and paralogous sequences, that is identical or similar codes across species or within one organism
• Convergent evolution describes the process whereby the same biological traits are acquired by lineages that are discrete.

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