Ka/Ks Evolutionary Divergence Time Calculator

Historical Background

The Ka/Ks ratio is a widely used measure in molecular evolution to understand the selective pressure acting on protein-coding genes. Ka (non-synonymous substitutions per site) and Ks (synonymous substitutions per site) represent changes that affect protein structure and neutral changes, respectively. By comparing the ratio of Ka to Ks, researchers can infer whether a gene is under purifying selection (Ka/Ks < 1), neutral evolution (Ka/Ks = 1), or positive selection (Ka/Ks > 1).

Calculation Formula

The formula for calculating evolutionary divergence time based on Ks and the mutation rate (\( r \)) is:
\[ \text{Evolutionary Time (Million Years)} = \frac{\text{Ks}}{2 \times r} \times 10^6 \]

Where:

• \( \text{Ks} \) is the synonymous substitution rate.
• \( r \) is the mutation rate (substitutions per site per year).

Example Calculation

If \( \text{Ks} = 0.02 \) and \( r = 1 \times 10^{-9} \):
\[ \text{Evolutionary Time} = \frac{0.02}{2 \times 1 \times 10^{-9}} \times 10^6 = 10 \, \text{million years}. \]

Importance and Usage Scenarios

• Studying Evolutionary History: Helps infer the time of divergence between two species or genes.
• Selection Pressure Analysis: Identifies whether genes are under selective pressure or evolving neutrally.
• Genetic Conservation Studies: Explores evolutionary constraints on protein-coding genes.

Common FAQs

1. What does Ka/Ks > 1 indicate?

   • It suggests positive selection, where non-synonymous changes are favored over synonymous changes.

2. Why is Ks used to estimate evolutionary time?

   • Ks changes are often considered neutral and accumulate at a constant rate, making them suitable for molecular clocks.

3. How do I determine the mutation rate?

   • Mutation rates can be obtained from literature or derived experimentally based on genome sequences and known divergence times.

This calculator is a powerful tool for evolutionary biologists to calculate divergence times and understand molecular evolutionary dynamics.