Local adaptation and archaic introgression shape global diversity at human structural variant loci

Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs...

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Autores principales:	Stephanie M Yan, Rachel M Sherman, Dylan J Taylor, Divya R Nair, Andrew N Bortvin, Michael C Schatz, Rajiv C McCoy
Formato:	article
Lenguaje:	EN
Publicado:	eLife Sciences Publications Ltd 2021
Materias:	positive selection immunoglobulin neanderthal insertion deletion eQTL Medicine R Science Q Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b54707afd69748fd9569c8f3c10b6a1f
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spelling	oai:doaj.org-article:b54707afd69748fd9569c8f3c10b6a1f2021-11-15T06:05:08ZLocal adaptation and archaic introgression shape global diversity at human structural variant loci10.7554/eLife.676152050-084Xe67615https://doaj.org/article/b54707afd69748fd9569c8f3c10b6a1f2021-09-01T00:00:00Zhttps://elifesciences.org/articles/67615https://doaj.org/toc/2050-084XLarge genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation – a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.Stephanie M YanRachel M ShermanDylan J TaylorDivya R NairAndrew N BortvinMichael C SchatzRajiv C McCoyeLife Sciences Publications Ltdarticlepositive selectionimmunoglobulinneanderthalinsertiondeletioneQTLMedicineRScienceQBiology (General)QH301-705.5ENeLife, Vol 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	positive selection immunoglobulin neanderthal insertion deletion eQTL Medicine R Science Q Biology (General) QH301-705.5
spellingShingle	positive selection immunoglobulin neanderthal insertion deletion eQTL Medicine R Science Q Biology (General) QH301-705.5 Stephanie M Yan Rachel M Sherman Dylan J Taylor Divya R Nair Andrew N Bortvin Michael C Schatz Rajiv C McCoy Local adaptation and archaic introgression shape global diversity at human structural variant loci
description	Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation – a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.
format	article
author	Stephanie M Yan Rachel M Sherman Dylan J Taylor Divya R Nair Andrew N Bortvin Michael C Schatz Rajiv C McCoy
author_facet	Stephanie M Yan Rachel M Sherman Dylan J Taylor Divya R Nair Andrew N Bortvin Michael C Schatz Rajiv C McCoy
author_sort	Stephanie M Yan
title	Local adaptation and archaic introgression shape global diversity at human structural variant loci
title_short	Local adaptation and archaic introgression shape global diversity at human structural variant loci
title_full	Local adaptation and archaic introgression shape global diversity at human structural variant loci
title_fullStr	Local adaptation and archaic introgression shape global diversity at human structural variant loci
title_full_unstemmed	Local adaptation and archaic introgression shape global diversity at human structural variant loci
title_sort	local adaptation and archaic introgression shape global diversity at human structural variant loci
publisher	eLife Sciences Publications Ltd
publishDate	2021
url	https://doaj.org/article/b54707afd69748fd9569c8f3c10b6a1f
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Local adaptation and archaic introgression shape global diversity at human structural variant loci

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