2021
DOI: 10.22541/au.162739700.00633111/v1
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The maintenance of standing genetic variation: gene flow versus selective neutrality in Atlantic stickleback fish

Abstract: Adaptation to derived habitats often occurs from standing genetic variation (SGV). The maintenance within ancestral populations of genetic variants favorable in derived habitats is commonly ascribed to long-term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favored in derived habitats are neutral in ancestral populations when their frequency is… Show more

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“…Raw sequences reads (Haenel et al, 2019b , 2021 ) were parsed by library (pool or individual) and aligned to the third‐generation stickleback reference genome assembly (Glazer et al, 2015 ) by using novoalign (version 4.0, http://www.novocraft.com/products/novoalign/ ; alignment settings provided in the Supplementary Codes). From the alignments, we derived nucleotide counts (pileups) for all genome‐wide positions by using the pileup function from the Rsamtools r package (Morgan et al, 2017 ; unless specified otherwise, all analyses were implemented with the r language, version 3.6.0; r Development Core Team, 2019 ).…”
Section: Methodsmentioning
confidence: 99%
“…Raw sequences reads (Haenel et al, 2019b , 2021 ) were parsed by library (pool or individual) and aligned to the third‐generation stickleback reference genome assembly (Glazer et al, 2015 ) by using novoalign (version 4.0, http://www.novocraft.com/products/novoalign/ ; alignment settings provided in the Supplementary Codes). From the alignments, we derived nucleotide counts (pileups) for all genome‐wide positions by using the pileup function from the Rsamtools r package (Morgan et al, 2017 ; unless specified otherwise, all analyses were implemented with the r language, version 3.6.0; r Development Core Team, 2019 ).…”
Section: Methodsmentioning
confidence: 99%