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

Abstract R package pcadapt is a user-friendly R package for performing genome scans for local adaptation. Here, we present version 4 of pcadapt which substantially improves computational efficiency while providing similar results. This improvement is made possible by using a different format for sto...

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Bibliographic Details
Published in:Molecular biology and evolution 2020-07, Vol.37 (7), p.2153-2154
Main Authors: Privé, Florian, Luu, Keurcien, Vilhjálmsson, Bjarni J, Blum, Michael G B
Format: Article
Language:English
Subjects:
Adaptation, Biological
Genomics - methods
Software
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Summary:Abstract R package pcadapt is a user-friendly R package for performing genome scans for local adaptation. Here, we present version 4 of pcadapt which substantially improves computational efficiency while providing similar results. This improvement is made possible by using a different format for storing genotypes and a different algorithm for computing principal components of the genotype matrix, which is the most computationally demanding step in method pcadapt. These changes are seamlessly integrated into the existing pcadapt package, and users will experience a large reduction in computation time (by a factor of 20–60 in our analyses) as compared with previous versions.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/msaa053