Maximum Likelihood Phylogeny Explained Simply with Example

Introduction

Maximum Likelihood phylogeny is a statistical method used to construct evolutionary trees from DNA data. It selects the tree that has the highest probability of producing the observed sequences under a specific evolutionary model. Therefore, it provides a strong mathematical framework for phylogenetic analysis. Today, researchers widely use this method in molecular systematics because it gives accurate and reliable results. You can easily download this note as a PDF using the link provided just below the post for quick access and offline reading.

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Definition

Maximum Likelihood phylogeny is a model-based statistical approach that estimates evolutionary relationships by selecting the tree that maximizes the likelihood of observing the given molecular data.

What Is Maximum Likelihood Phylogeny?

Maximum Likelihood phylogeny works on one key principle:

Choose the evolutionary tree that makes the observed DNA data most probable.

In simple words, the method asks:

If this tree were true, how likely would we observe this DNA sequence data?

The tree with the highest likelihood value is selected as the best tree.

Unlike Maximum Parsimony, which focuses on the fewest changes, this method evaluates probability using mathematical models.

How Maximum Likelihood Phylogeny Works

The process follows several clear steps.

1. Collect Molecular Data

Researchers first obtain aligned DNA sequences. In plant studies, common genes include:

• rbcL
• matK
• ITS region

These markers provide variation needed for evolutionary comparison.

2. Select an Evolutionary Model

Next, scientists choose a substitution model. This model describes how DNA changes over time.

• Jukes–Cantor model
• Kimura 2-parameter model
• GTR (General Time Reversible) model

Choosing the correct model improves accuracy. Therefore, model testing is an important step.

3. Calculate Likelihood Values

The software evaluates many possible trees.

For each tree, it:

• Applies the evolutionary model
• Calculates the probability of the observed data
• Assigns a likelihood score

The tree with the highest score is selected.

Because the number of possible trees is very large, software tools perform complex computations.

Popular programs include:

• MEGA
• RAxML
• PhyML

These programs efficiently analyze large molecular datasets.

Interpretation of Results

Maximum Likelihood phylogeny produces:

• A best-supported tree
• Branch lengths
• Likelihood scores
• Bootstrap support values

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Bootstrap values help measure confidence in clades.

• Above 90% → Strong support
• 70–89% → Moderate support
• Below 70% → Weak support

Thus, researchers can evaluate the reliability of evolutionary relationships.

Example from Plant Systematics

Consider a study on the genus Solanum.

• Solanum tuberosum (potato)
• Solanum melongena (brinjal)
• Solanum lycopersicum (tomato)

Researchers analyze the rbcL gene using RAxML.

The Maximum Likelihood phylogeny may show:

• Potato and tomato cluster together
• Brinjal forms a sister group
• Strong bootstrap support above 90%

Therefore, scientists conclude these species share a recent common ancestor.

This method helps taxonomists:

• Confirm evolutionary relationships
• Revise plant classifications
• Detect monophyletic groups

Comparison with Other Methods

Method	Principle	Output
Maximum Parsimony	Fewest evolutionary changes	Single simplest tree
Bayesian Inference	Posterior probability	Set of probable trees
Maximum Likelihood	Highest likelihood value	Best statistical tree

Advantages of Maximum Likelihood Phylogeny

• Statistically robust
• Uses realistic evolutionary models
• Handles complex DNA datasets
• Estimates branch lengths accurately

Limitations

• Computationally intensive
• Sensitive to model choice
• Can be slow with very large datasets

Conclusion

In summary, Maximum Likelihood phylogeny is a statistically strong method for constructing evolutionary trees. It selects the tree that best explains observed DNA data under a chosen model. As a result, it provides reliable and scientifically sound evolutionary interpretations. For students of molecular biology and plant systematics, understanding Maximum Likelihood phylogeny is essential for modern phylogenetic analysis.

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