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Phylogenetic and Phylogenomic Analysis

Phylogenetics is the scientific study of the evolutionary relationships between various organisms via sequencing the molecular data and morphological data matrices. This scientific field is mainly concerned with the relationships of organisms with one another on the basis of evolutionary similarities and differences. The word “Phylogenetics” has been derived from two Greek words, Phylon/Phlye meaning “tribe/race”, and Genetekos meaning “relative to birth”.

Phylogenetics is a part of biological systematics and involves the identification and classification of organisms (Taxonomy). Phylogenetics implies the usage of DNA/RNA/protein sequencing techniques to analyze the observable inheritable and heritable traits. In Phylogenetics studies, a tree-like diagram is used to generate and locate the hypothetical evolutionary relationships and histories of groups of organisms according to phylogenies of various biological species. The phylogenetic tree has been used to understand biodiversity, genetics, evolutions, and ecology of organisms.

Types of queries phylogeneticists work on

A phylogeneticist might study one of the following queries:

  1. What are the evolutionary relationships or histories among my species/individuals/genes of interest?

  2. How do sequences evolve?

  3. Can I better describe processes of sequence evolution with a mathematical model?

To reconstruct a phylogenetic tree, we can use the nucleotide or protein sequences combined with our understanding of sequence evolution using an evolutionary model. This allows us to infer evolutionary events that might have happened in the past and provides more detailed information about the evolutionary process based on the molecular data. Thereby, we can refine our evolutionary knowledge and develop better mathematical models for evolutionary analysis.

Why do we use molecular data for phylogenetic analysis?

This is due to the following reasons:

  • DNA is the inherited material;

  • We can now easily, quickly, inexpensively and reliably sequence the genetic material;

  • Sequences are highly specific and are often information rich and are being utilized as more reliable biological fossils.

In a very few and rare cases, where it is not possible to obtain genetic material (e.g. in the case of certain ancient fossil samples), morphological measurements can be used to infer evolutionary relationships. However, this approach is less reliable than using molecular data because we know that sometimes the same morphological trait can arise from multiple independent evolutionary lineages.

Importance of Phylogenetics

It is an important field, because it enriches our understanding of how genes, genomes, species (and molecular sequences more generally) have evolved. Through phylogenetics, we came to know, not only how the sequences came to be the way they are today, but also general principles that enable us to predict how they will change in the future. This is not only of fundamental importance but also extremely useful for numerous applications, which includes:

  • Classification: On the basis of sequence data, Phylogenetics provides us with more accurate descriptions of patterns of relatedness than was available before the advent of molecular sequencing. Phylogenetics now informs the Linnaean classification of new species.

  • Forensics: It is being utilized to assess DNA evidence presented in court cases to inform situations, e.g. where someone has committed a crime, when food is contaminated, or where the father of a child is unknown.

  • Identifying the origin of pathogens: Phylogenetic approaches along with the molecular sequencing technologies can be used to learn more about a new pathogen outbreak. This includes finding out about which species the pathogen is related to and subsequently the likely source of transmission. This can lead to new recommendations for public health policy.

  • Conservation: Phylogenetics studies can help the conservation scientists to inform conservation policy when they have to make tough decisions about which species they try to prevent from becoming extinct.

  • Bioinformatics And Computing: Many of the algorithms developed for phylogenetics have been used to develop software in other fields.

  • Future Applications: With the advent of newer, faster sequencing technologies, it is now possible to take a sequencing machine out to the field and sequence species of interest in situ. Phylogenetics is needed to add biological meaning to the data.

Stages in Phylogenetics Analysis

There are no hard and fast steps for the study of phylogenies, it ultimately depends upon the biological question of interest. However, some major stages are discussed here:

  1. Start with a question.

  2. Identify a model and parameters that could possibly answer the question.

  3. Collect sequence data that would help to answer the question.

  4. Identify the orthologous sequences.

  5. Sequence alignment.

  6. Estimate tree and other parameters given the data and model.

  7. Estimate the error associated with the tree and the parameter estimates.

  8. Does it answer your question?

  9. New biological insight.


The field of science that studies the relationship of the function of genes to their evolution. It comprises of several areas of research at the interface between molecular and evolutionary biology and has two major goals:

  1. To infer phylogenetic relationships between taxa and gain insights into the mechanisms of molecular evolution.

  2. To use multispecies phylogenetic comparisons to infer putative functions for DNA or protein sequences.

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