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EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection
Author(s) -
Qi GuoAn,
Zheng YuanTing,
Lin Feng,
Huang Xin,
Duan LiWen,
You Yue,
Liu Hailan,
Wang Ying,
Xu HaiMing,
Chen GuoBo
Publication year - 2021
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.13370
Subject(s) - biology , selection (genetic algorithm) , population , natural selection , computer science , graphical user interface , machine learning , data mining , computational biology , artificial intelligence , demography , sociology , programming language
Detecting genetic regions under selection in structured populations is of great importance in ecology, evolutionary biology and breeding programmes. We recently proposed EigenGWAS, an unsupervised genomic scanning approach that is similar to F ST but does not require grouping information of the population, for detection of genomic regions under selection. The original EigenGWAS is designed for the random mating population, and here we extend its use to inbred populations. We also show in theory and simulation that eigenvalues, the previous corrector for genetic drift in EigenGWAS, are overcorrected for genetic drift, and the genomic inflation factor is a better option for this adjustment. Applying the updated algorithm, we introduce the new EigenGWAS online platform with highly efficient core implementation. Our online computational tool accepts plink data in a standard binary format that can be easily converted from the original sequencing data, provides the users with graphical results via the R‐Shiny user‐friendly interface. We applied the proposed method and tool to various data sets, and biologically interpretable results as well as caveats that may lead to an unsatisfactory outcome are given. The EigenGWAS online platform is available at www.eigengwas.com , and can be localized and scaled up via R (recommended) or docker .