iMKT: the integrative McDonald and Kreitman test

Area of Science:

• Evolutionary Biology
• Population Genetics
• Bioinformatics

Background:

• The McDonald and Kreitman test (MKT) is crucial for detecting natural selection using DNA sequence data.
• Existing methods may lack the integrative capacity to analyze diverse selection regimes simultaneously.

Purpose of the Study:

• Introduce iMKT, a novel web-based service for performing multiple types of the McDonald and Kreitman test.
• Enable the detection and estimation of various selection regimes (adaptive, neutral, deleterious) on genomic sequences.

Main Methods:

• Developed a web-based service implementing four distinct MKT variations.
• Integrated analysis of user-provided population genomic data.
• Included pre-loaded datasets for Drosophila melanogaster and human protein-coding genes from large-scale population genomics studies.

Main Results:

• iMKT allows for the detection and estimation of adaptive, neutral, strongly deleterious, and weakly deleterious selection.
• The tool supports analysis of both custom and existing genomic datasets.
• Advanced options facilitate testing complex evolutionary hypotheses, such as the relationship between recombination rates and adaptation.

Conclusions:

• iMKT provides a comprehensive platform for studying evolutionary adaptation in population genomics.
• It is particularly valuable for large datasets, especially in model organisms like Drosophila and humans.
• The tool aims to be a reference resource for evolutionary studies.