Performing Highly Efficient Genome Scans for Local Adaptation with R Package pcadapt Version 4.

Area of Science:

• Population Genetics
• Bioinformatics
• Genomics

Background:

• The pcadapt R package facilitates genome scans to identify genetic markers associated with local adaptation.
• Computational efficiency has been a limiting factor in analyzing large genomic datasets for adaptation.

Purpose of the Study:

• To introduce version 4 of the pcadapt R package, focusing on substantial improvements in computational efficiency.
• To maintain the accuracy of results while reducing computation time for genome scans.

Main Methods:

• Implementing a new genotype storage format.
• Utilizing an optimized algorithm for computing principal components of the genotype matrix.
• Integrating these changes seamlessly into the existing pcadapt package.

Main Results:

• Achieved a significant reduction in computation time, ranging from 20-60 fold in analyses.
• Ensured that the results obtained are comparable to previous versions of the package.
• Demonstrated seamless integration of the new computational methods.

Conclusions:

• Version 4 of pcadapt offers a highly efficient tool for genome scans of local adaptation.
• Researchers can now analyze larger genomic datasets more rapidly without compromising accuracy.
• The updated package provides a substantial performance improvement for population geneticists and bioinformaticians.