The word phylogenetics is derived from Greek word phyle and genetikos.Phyle means tribe and genetikos means origin or birth so phylogenetics is a study of origin of tribes or the study of exploring the evolutionary connections among living organisms[1]. Phylogenetic analysis means analyzing how organisms and their characters evolved over time. This analysis also tells the evolutionary relationships between different species and macromolecules like proteins and genes. Phylogenetic analysis is done by collecting data from various organisms, data can be protein or DNA sequences, aligning the sequences using multiple sequence alignments to identify homology between sequences and ensure correct phylogenetic analysis, constructing a phylogenetic tree for visualizing the relationship between species and then inferring the tree for finding clades and evolutionary cascade.
Applications of phylogenetic Analysis:
1.Identification of beneficial mutations during evolution:
Phylogenetic analysis helps in determining the new functions of genes that occurred by beneficial mutations in sequences. By analyzing the gene or protein sequences of ancestral organisms, evolutionary biologists are able to identify the amino acids or nucleotide substitutions that occur during evolution and result in new functions of genes and proteins.
TRIM5a gene evolution:
Evolutionary biologist has detected that TRIM5a gene which is innate immune gene undergoes evolutionary change to become species specific and become effective for defending against viruses in different species. Also, they are revolutionized to recognize different viral capsid structures. By applying phylogenetic analysis, biologists are able to reveal how TRIM5a has evolved to fight against viral infections such as retroviruses (HIV-1) in different species. With the evolution of virus strategies to infect, TRIM5a also adapted to fight with new strategies. Phylogenetic analysis unveils the evolutionary history and beneficial mutations by reconstructing ancestral sequences of TRIM5a gene (antiviral gene).[2].
2.Evolutionary secrets of viruses leading to effective counter measures:
Phylogenetic analysis also helps biochemists and virologist to understand viral evolutions. By knowing evolutionary history, researchers gain deep perception of what type of mutations occur with time. How these mutations evolved viral function and mechanism of viral transmission. By knowing phylogenetic dynamics, researchers develop new strategies and effective vaccines to combat various viral strains.
Phylogenetic Analysis of Canine parvovirus:
Canine parvovirus is a DNA virus that infect canines and is emerged from feline panleukopenia parvovirus (FPLV) or by recombination of related viruses. Its evolution rate is very high just like RNA viruses. Mutations in CPV with time results in its different stains ,differing in its virulence and host[3].Such genomic diversity in CPV help biologists to predict future evolution in viruses and developing proactive treatments.
3.Prediction of ancestral protein sequences:
Phylogenetic analysis helps to reconstruct most likely ancestral sequences by inferring DNA and protein sequences of their Descendants. Predicting ancestral sequences tells us about how proteins evolved over time. By comparing ancestral sequences with modern sequences , we are able to detect the specific amino acids whose substitution results in functional changes. This also helps protein engineers for finding the functional residues over time and modifying them for desired functions. Phylogenetic analysis of proteins also gives information about origin of protein families like most important globin gene family. Analysing globin genes from different organisms , it explores evolutionary relation ship between them. Also revealing haemoglobin share common ancestor with globin gene family by undergoing evolutionary innovations[4]
4.Prediction of molecular evolution:
Phylogenetic analysis helps researchers in molecular evolution genomics to detect positive changes in DNA coding region for protein synthesis. By constructing phylogenetic tree of related organisms and comparing DNA sequences enables identification of synonymous and non synonymous changes occurred in protein over time. Also discovering whether specific non synonymous changes modify our ancestors to adapt to their environment. Phylogenetic analysis of Human Leukocytes Antigen (HLA)gene allows detection of positive selection which forms the basis of its evolution in immune system to fight disease in better way . Two main methods: Parsimony method and likelihood method are used estimate the rate of different types of changes and correctly identify sites under positive selection.[5]
Conclusion:
Phylogenetic analysis act as powerful tool for understanding dynamics of evolutionary changes. Using its applications in field of medicine , agriculture and biotechnology ,it informs researchers to develop advanced vaccines and design proteins with desired functions. By refining further phylogenetic analysis techniques , we can harness its power for real world challenges of 21st centuries. It will continue to craft future scientific researches by dealing with global challenges from infectious out break to climate change.
Reference:
1. Roy, S.S., R. Dasgupta, and A. Bagchi, A review on phylogenetic analysis: a journey through modern era.Computational Molecular Bioscience, 2014. 4(03): p. 39.
2. Sawyer, S.L., et al., Positive selection of primate TRIM5 α identifies a critical species-specific retroviral restriction domain.Proceedings of the National Academy of Sciences, 2005. 102(8): p. 2832-2837.
3. Shackelton, L.A., et al., High rate of viral evolution associated with the emergence of carnivore parvovirus.Proceedings of the National Academy of Sciences, 2005. 102(2): p. 379-384.
4. Storz, J.F., J.C. Opazo, and F.G. Hoffmann, Phylogenetic diversification of the globin gene superfamily in chordates.IUBMB life, 2011. 63(5): p. 313-322.
5. Suzuki, Y. and T. Gojobori, A method for detecting positive selection at single amino acid sites.Molecular biology and evolution, 1999. 16(10): p. 1315-1328.
