7 Biosystematics

7.3 Phylogenetics

Phylogenetics

Dr V Malathi

The study of evolutionary relationships among organisms is called Phylogenetics. It reconstructs the evolutionary history of species and charts their relationships in a phylogenetic tree using genetic, morphological, and biochemical data. Understanding the relationships between species, the history of their evolutionary divergence, and the evolution of features across time is made easier by phylogenetics.

Phylogenetic Trees

To illustrate the evolutionary relationships and paths between organisms, scientists employ a particular kind of model known as a phylogenetic tree  also called as evolutionary trees. It is an illustration of the evolutionary links between individuals or groups of organisms  . As the suggested linkages cannot be verified in the past, scientists view phylogenetic trees as a hypothesis of the evolutionary past.

Terminology that characterizes a phylogenetic tree.

The lines in the tree are called branches. Branches on the tree indicate lineages of organisms. At the tips of the branches are present-day species or sequences known as taxa (the singular form is taxon) or operational taxonomic units.The connecting point where two adjacent branches join ( branch point) is called a node, which represents a common ancestor.In a phylogenetic tree, closely related organisms are joined by nodes. These nodes suggest common ancestry.  two taxa stemming from the same most recent node are called  sister taxa.
Rooted and Unrooted trees 

A common ancestor is represented by a single lineage at the base of many phylogenetic trees. Such trees are referred  as rooted phylogenetic tree, indicating that all of the creatures shown in the diagram are related to a single ancestral lineage, usually drawn from the bottom or left. The three domains of bacteria, archaea, and eukarya branch off from a single point in the rooted phylogenetic tree.In this image, the little branch that plants and animals—including humans—occupy demonstrates how recent and insignificant these groupings are in relation to other species. Unrooted  phylogenetic trees reveal links between species but not a common ancestor.

Clade or monophyletic group 

A group of taxa descended from a single common ancestor is defined as a clade or monophyletic group. In a monophyletic group, two taxa share a unique common ancestor not shared by any other taxa. They are also referred to as sister taxa to each other (e.g., taxa B and C). Example: In mammals, the clade of primates includes humans, chimpanzees, gorillas, and all other primates with their common ancestor.
The branch path depicting an ancestor–descendant relationship on a tree is called a lineage. 
Paraphyletic group
When a number of taxa share more than one closest common ancestors, they do not fit the definition of a clade.In this case, they are referred to as paraphyletic (e.g., taxa B, C, and D).
File:Taxonomy and phylogenetics.svg

Tree topology

The branching pattern in a tree is called tree topology. When all branches bifurcate on a phylogenetic tree, it is referred to as dichotomy. In this case, each ancestor divides and gives rise to two descendants.
Sometimes, a branch point on a phylogenetic tree may have more than two descendents, resulting in a multifurcating node. The phylogeny with multifurcating branches is called polytomy. A polytomy can be a result of either an ancestral taxon giving rise to more than two immediate descendants simultaneously during evolution, a process known as radiation, or   an unresolved phylogeny in which the exact order of bifurcations cannot be determined precisely

Forms of Tree Representation 

Phylogram and Cladogram

The topology of branches in a tree defines the relationships between the taxa. The trees can be drawn in different ways, such as a cladogram or a phylogram.
In a phylogram, the branch lengths represent the amount of evolutionary divergence. Such trees are said to be scaled.The scaled trees have the advantage of showing both the evolutionary relationships and information about the relative divergence time of the branches.
In a cladogram, however, the external taxa line up neatly in a row or column. Their branch lengths are not proportional to the number of evolutionary changes and thus have no phylogenetic meaning. In such an unscaled tree, only the topology of the tree matters, which shows the relative ordering of the taxa.

Molecular Phylogenetics:

enables researchers to track lineages back to common ancestors by analyzing evolutionary relationships using DNA, RNA, or protein sequences.
Molecular techniques have transformed phylogenetics by offering information that helps elucidate connections in situations when morphological evidence is unclear or lacking.

Methods of Building Phylogenetic Trees

  1. Distance Methods:
    • These methods create a tree based on overall similarity.These techniques determine the genetic distance between two sequence pairs.
    • Neighbor-joining is a popular distance method  that reduces the tree’s overall branch length.
  2. Maximum Parsimony:
    • This approach assumes that simpler evolutionary pathways are more plausible than complex ones, and it looks for the tree with the fewest evolutionary changes.
  3. Maximum Likelihood and Bayesian Methods:
    • The Bayesian and maximum likelihood statistical techniques determine the likelihood of a specific tree given an evolutionary change model.
      While Bayesian approaches predict a range of plausible topologies, Maximum Likelihood uses sequence data to determine which tree has the highest likelihood.

Applications of Phylogenetics

  1. Classification and Taxonomy: Contributes to the improvement of the biological categorization system by grouping species according to evolutionary links.
  2. Understanding Evolutionary History: The chronology and order of evolutionary events, including speciation and trait development, can be known by an understanding of evolutionary history.
  3. Tracking Disease Evolution: This method is used in epidemiology to investigate the causes and dissemination of infections, including monitoring the genetic development of viruses such as SARS-CoV-2 and HIV.
  4. Conservation Biology: Assists in identifying evolutionary distinct species that, because of their distinct genetic heritage, may be conservation priorities.
  5. Comparative Genomics: Phylogenetics helps to compare genomes across species, identify conserved genes, and to study gene function and evolution.

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