Tracking Lineage: Character Based Phylogenetic Study

Tracking Lineage: Character Based Phylogenetic Study

The question ‘where did it all start?’ often intrigued the human brain and the answer to this question led to a new entity called phylogenetics. The study of biological life with respect to evolutionary relations which assists in tracking their lineage and to analyze the shared progenitors is specified as phylogenetics. [i]One of the prime objectives of phylogenetics is the visual delineation of relationships by assembling a phylogenetic tree and the character-based methods for phylogenetic study are prominent for their ability to inspect particular traits and precisely analyze genomic data. 

Character based methods:

Phylogenetic character methods deduce evolutionary relationships by the use of analytical techniques for distinct features of species. These traits can be molecular (nucleotide or protein), morphological or behavioral.[ii]The character-based methods do not rely on pairwise distance differentiation rather they are able to analyze the sequence data instantaneously by scrutinizing the sequence characters.  These methods are regarded to be more precise and accurate than distance-based methods. Let’s plunge into the details and importance of these methods.

1. Maximum Parsimony Method (M.P): Maximum Parsimony constructs phylogenetic trees with least evolutionary changes as it is rooted in the concept of simplicity and this makes it stand out from others. The principle of parsimony is the foundation for this method, which is also mentioned as Occam’s razor and it suggests that the simplest statement is the most accurate. During the operation, each one of the characters is examined across all species and the tree with least character swaps is considered the finest hypothesis for evolutionary history by Maximum Parsimony method. [iii]

Course of Action: Character selection and coding are one of the first steps of Maximum Parsimony and each taxon is explained by a set of characters. Then, feasible trees are put together which is followed by allotting a score to each tree on the grounds of the number of changes noticed in the character states and the most parsimonious tree is decided, the one with the fewest changes. 

With all its precedence, Maximum Parsimony is equipped with some limitations and the most rudimentary is the loss of information due to minimizing changes and the occurrence of homoplasy which can lead to a faulty tree.

2. Maximum Likelihood Method (M.L): Maximum Likelihood method stands in the race for character-based methods. The word ‘likelihood’ is mentioned to be the probability that under a certain model of evolution a specific evolutionary tree is formulated using the distinguished data. Under the ambience of phylogenetics, Maximum Likelihood is well suited for examining large and complex datasets along with concluding most probable phylogenetic tree dependent on genome sequences or some other character data. 

Course of Action: This method revolves around the likelihood calculations, but first a pertinent model of evolution is decided which narrates the character modifications over the time. Secondly, an inchoate phylogenetic tree is mapped out which is trailed by the statistical calculations to generate an explicit phylogenetic tree which is then assessed through bootstrapping.  [iv]

The restrictions to this procedure are associated with its computational intensity which becomes overwhelming with increased data together with extra time consumption. 

3. Bayesian Inference Method:   Bayes’ Theorem presented us with Bayesian Inference method, which explains the practice of updating the probability of postulates as more evidence is collected. In phylogenetics, Bayesian Inference helps in approximating posterior probability of an evolutionary tree as it incorporates the prior probability distribution.[v]This method offers a powerful replacement for traditional methods as it is harnessed under the principle of probability and statistics for mapping out the tree of life.

Course of Action: As Maximum Likelihood, Bayesian Inference outsets with the choice of an evolutionary model with prior probability distribution which is then treated with algorithms to initiate posterior probabilities for nuanced conclusions to infer a realistic evolutionary tree.

Challenges and Future Directions: 

Meanwhile character methods are considered influential tools for phylogenetic exploration, they are also accompanied with some drawbacks. One of the fundamental challenges is computational intricacy, advancements in computational algorithms and methods can efficiently improve the precision of these methods. Moreover, the other obstacle is the germane selection of evolutionary models as Maximum Likelihood and Bayesian method are very reliant on the chosen model. 

Conclusion:

Character based methods of phylogenetics are the source for developing pedigree which elucidates the evolutionary relation among species. As these methods proceed with their progress, the combination of genomic data and computational methods will expound the tree of life and reveal the processes that have sculpted the diversity of life.  

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