Difference Between UPGMA and Neighbor Joining Tree

The key difference between UPGMA and neighbor joining tree is the type of the phylogenetic tree resulting from each method. UPGMA is the technique of constructing a rooted phylogenetic tree while neighbor joining tree is the technique of constructing an unrooted phylogenetic tree.

Phylogenetic trees are tree-like diagrams that show evolutionary relationships between organisms. A phylogenetic tree can have different topologies depending on the technique used for tree construction. UPGMA and neighbor joining tree are two main methods that build phylogenetic trees.

CONTENTS

1. Overview and Key Difference
2. What is UPGMA 
3. What is Neighbor Joining Tree
4. Similarities Between UPGMA and Neighbor Joining Tree
5. Side by Side Comparison – UPGMA vs Neighbor Joining Tree in Tabular Form
6. Summary

What is UPGMA?

In bioinformatics, there are different clustering techniques. UPGMA stands for Unweighted Pair Group Method and Arithmetic Mean. It is a hierarchical grouping method. The method was introduced by Sokal and Michener. It is the fastest technique that develops a phylogenetic tree. The resulting phylogenetic tree is a rooted phylogenetic tree with a common ancestor.

When drawing a phylogenetic tree using the UPGMA method, it considers evolutionary rates as the same for all the lineages. Thus, this is an important assumption made in the UPGMA technique. However, this is also the main drawback of the technique as mutation rate is not considered during the tree construction. Instead, it assumes the mutation rate as a constant. Further, this hypothesis is termed as the “Molecular clock hypothesis”. Therefore, in the real context, the phylogenetic tree constructed from a UPGMA method may not be accurate and reliable.

UPGMA method considers pair-wise distances to produce a phylogenetic tree. Initially, each species is a cluster, and two such clusters with the smallest evolutionary distance form a pair. Therefore, it depends on the distance matrix. Algorithm expressions play a major role in interpreting the data of a phylogenetic tree drawn using the UPGMA method.

What is Neighbor Joining Tree?

Neighbor Joining Tree is another clustering technique used to produce a phylogenetic tree. Naruya Saitou and Masatoshi Nei were the pioneers in introducing the method. The technique produces an unrooted tree, unlike UPGMA. Furthermore, the clustering in this method does not rely on ultrametric distances. However, it considers the variation of evolutionary rates when constructing the phylogenetic tree. Thus, there are variations in the trees drawn using this technique. Therefore, this method uses special mathematical algorithms to assess those variations.

When constructing the trees, this method considers the distances between each lineage separately. Each lineage joins the newly constructed node in the tree. All of these nodes join the central node. Therefore, when a new node appears, the distance from the central node to the new node is important and is calculated using the algorithms. These algorithmic data decide the placement of the new node.

What are the Similarities Between UPGMA and Neighbor Joining Tree?

• Both methods use clustering techniques when constructing phylogenetic trees.
• Moreover, both methods require the use of mathematical algorithms to interpret the phylogenetic tree.
• DNA sequence data play an important role in both methods.
• Both methods result in a bottom-up clustering method.
• Moreover, analysis of large data sets is possible using both techniques.
• Statistical data analysis can be applied for both types of trees using the bootstrap method.
• Both play an important role in the classification and identification of organisms.
• Moreover, both methods provide data on the evolutionary relationships of organisms.

What is the Difference Between UPGMA and Neighbor Joining Tree?

The key difference between UPGMA and neighbor joining tree relies on the type of tree constructed. So, UPGMA produces a rooted tree while neighbor joining tree produces an unrooted tree. Moreover, UPGMA is a less reliable method while neighbor joining tree is a reliable method than UPGMA. So, this is another difference between UPGMA and neighbor joining tree.

The below info-graphic summarizes the difference between UPGMA and neighbor joining tree.

Summary – UPGMA vs Neighbor Joining Tree

UPGMA and neighbor joining tree methods are two techniques that are important during the construction of a phylogenetic tree. While the UPGMA method does not consider the evolutionary rate, the neighbor joining method considers it during the tree construction. Thus, the complexity and the reliability of the phylogenetic tree resulting from the NJ tree method is high. However, it is not as rapid as the UPGMA method. Moreover, the key difference between UPGMA and neighbor joining tree relies on the type of tree resulting from each technique. UPGMA results in a rooted phylogenetic tree while neighbor joining tree method results in an unrooted phylogenetic tree.

Reference:

1. Pavlopoulos, Georgios A, et al. “A Reference Guide for Tree Analysis and Visualization.” BioData Mining, BioMed Central, 22 Feb. 2010, Available here.

Image Courtesy:

1. “CCDC138 rooted phylogeny tree” By Kokxx012 at English Wikipedia (CC BY-SA 3.0) via Commons Wikimedia
2. “Figure 5” By PLOS ONE PHYLOGENY (CC BY 2.0) via Flickr