What is Phylogenetics?

Phylogenetics is the scientific study of how various groups of organisms are related at the evolutionary level. It finds the relationship between various organisms based on their evolutionary similarities and differences. It is a part of the taxonomy. Although the taxonomic study is not only concerned about phylogeny but taxonomic studies are also concerned about the classification and nomenclature of the different individuals from different taxon.

Importance of Phylogenetics

At the molecular level, evolution is observable as changes in nucleotides in the nucleic acid and changes in amino acids in proteins. Therefore, in phylogenetic studies, DNA (Deoxyribonucleic acid), RNA (Ribonucleic acid), and proteins are 'information molecules' because they retain information about an organism's evolutionary history. In this case, nucleic acid and protein sequences of different organisms are compared using computer programs. Then the evolutionary relationship is estimated based on the degree of homology between the sequences. When differences arise in the nucleotide sequences within a gene or amino acid sequences within a protein, it reflects that two organisms are evolutionarily distanced. This means that closely related organisms exhibit almost similar sequences or fewer different sequences than distantly related organisms. Thus, the field of phylogenetics can be defined as the study of the evolutionary closeness of genes or proteins by analyzing mutations at various positions in their sequences and developing a hypothesis about how biomolecules are related. Phylogenetic studies construct the tree-like pattern that describes the relations of evolution among the species being studied.

Phylogenetic Tree

Phylogenetic trees are the graphical representation of the evolutionary relationship between a group of organisms used in a phylogenetic study. It is a two-dimensional graph showing relations of evolution among species or genes from various species. It is represented by branches and nodes. Nodes may be internal or external. The internal one represents the last common ancestor of the two lineages. External nodes or terminal nodes or leaves or operational taxonomic units (OTUs) represent the tip of the tree. Similarly, branches can be internal or external. In the case of external branches, they connect a tip and a node. On the other hand, two nodes are connected by internal branches or internodes.

Types of Phylogenetic Trees

A phylogenetic tree may be rooted or unrooted due to phylogenetic diversity.

  • A rooted tree infers the existence of phylogenetic systematics i.e., a common ancestor from which all the outer species originate and indicates the direction of the evolutionary process. A binary tree is a rooted tree in which every node has two descendants.
  • An unrooted tree does not provide any information about the phylogenetic system for their common ancestor and shows only the relations of evolutions among the species. Most trees of phylogeny are rooted and show the maximum likelihood of species.

Construction of Phylogenetic Tree

A phylogenetic tree can be drawn in different ways. The branches can either be scaled, that is, their lengths proportional to the extent of changes in evolution. On the other hand, unscaled branches have lengths that convey particular information. In trees with unscaled branches, the branch length is not proportional to the number of changes. The branching pattern of the tree is called topology. Trees of phylogenetics can be depicted in different ways, which provides the actual concept of phylogenetics and helps researchers to understand the mechanisms of the phylogeny and the history of evolutionary relationships between different species.

Selection of Molecular Markers

In a phylogenetic study, to construct a phylogenetic tree, it is necessary to compare nucleic acid sequences within a gene or amino acid sequences within a protein. The process of sequencing nucleotides or proteins is dependent on their characteristics and the purpose for which they are to be sequenced. The phylogenetic information of nucleic acid sequences is more than that of protein sequences. Because silent mutations can alter sequences without altering the amino acid and thus helps to create different taxon in phylogeny. Hence, in phylogeny, studying very closely related species, different taxon, nucleotide sequences, which evolve more rapidly than proteins, can be used. If the phylogenetic relation is to be delineated at the deepest level between two distinct groups of the taxon, such as between bacteria and eukaryotes, using conserved protein sequences makes more sense than using nucleotide sequences because of degeneracy in genetic codes. Amino acid sequences in a protein are more conserved, while DNA sequence becomes changed. As a result, in terms of phylogeny, variations occur in DNA sequences more often than protein sequences.

Process of Selection

The evolutionary history of maximum likelihood species and the phylogenetic diversity can be determined using molecular phylogenetics. The nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) have been most commonly used for phylogenetic studies. The molecular data derived from DNA sequences chosen for phylogenetic analysis must display variability in the organism being studied. If there is no variability in the DNA-based data, then there is no information present related to phylogeny.

For example, for evolutionary analysis of different individuals within a population or species belonging to similar phylogenetic systematics, mtDNA is often used. mtDNA is known to evolve much faster than the nuclear genome. Consequently, mtDNA has been used mostly to examine phylogenetic relationships in relatively lower categorial levels such as families, genera, species, or populations. Although mtDNA has evolved faster than nuclear genomic contents i.e., nuclear DNA, 12S rRNA (ribosomal RNA), however, is highly conserved. For studying phylogeny and the evolution of more divergent groups of species, one may choose either slowly evolving nucleotide sequences, such as nuclear rDNA or protein sequences. 

Molecular Clock

This hypothesis was originally proposed by researchers Emile Zuckerkandl and Linus Pauling based on empirical observations. But soon received theoretical backing when biologist Motoo Kimura developed the natural theory of evolution in 1968. Rates and amounts of genetic variation can be measured. It can be estimated from the amino acid sequence of a protein or nucleotide sequence of a region of DNA in two or more species. It is a technique to relate the time that the two species diverged to the number of molecular differences measured between the species' sequences of DNA or proteins. It is sometimes called a Gene clock or Evolutionary clock.  This concept is based on the hypothesis that DNA and protein sequences evolve at a rate that is relatively constant over time and among different organisms. This constancy is used to estimate the length of time that various organisms have been diverging from one another by measuring the degree of difference between two sequences.  

Gene Trees Versus Species Trees

In phylogenetics, these two are the two main pillars of phylogenetic studies. The representation derived from the genetic sequence is known as gene phylogeny, while the representation of the evolutionary path of the species is often referred to as species phylogeny. In a strict sense, a gene phylogeny only describes the evolution of that particular gene or encoded protein. The first one depicts the history of the evolution of a given gene or genetic changes related to that gene. It is reconstructed from comparisons between the sequence and orthologous genes. It can provide evidence for gene duplication and divergence events. It describes how a gene evolves through duplication, loss, and nucleotide substitution. The second one depicts the pattern of branching of species lineage via the process of speciation. It occurs by mutation and therefore it is referred to as one of the most essential causes of the generation of a tax on. Speciation occurs by the population of the ancestor species splitting into two groups that are unable to interbreed. An internal node in a gene tree indicates the divergence of an ancestral gene into two genes with different DNA sequences, this occurs by mutation but in the case of the species tree, it represents what is called speciation event, the most important part of the phylogenetic study, whereby the population of the ancestor species splits into two new groups that are no longer to interbreed. In phylogenetics, these two events, mutation, and speciation do not always occur at the same time.


r = D/2t


  • r= Number of substitutions per lineage per million years
  • D= Proportion of base pairs that differ between the two sequences
  • t= time of most recent common ancestor in million years

Context and Applications

This topic is significant in the professional exams for both under-graduate and post-graduate courses, especially for

  • B.Sc. in Biological Sciences
  • M. Sc. in Biological Sciences
  • B. Sc. in Zoology
  • M. Sc. in Zoology
  • M. Sc. in Molecular Biology
  • M. Sc. in Biophysics
  • Natural theory of evolution
  • Natural selection
  • Species concept
  • Geological time scale

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