A Genomic Map of the Effects of Linked Selection in Drosophila

PLoS Genetics
Eyal ElyashivGuy Sella

Abstract

Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of "linked selection" on levels of genetic diversity is key to making reliable inference about demography, building a null model in scans for targets of adaptation, and learning about the dynamics of natural selection. Here, we introduce the first method that jointly infers parameters of distinct modes of linked selection, notably background selection and selective sweeps, from genome-wide diversity data, functional annotations and genetic maps. The central idea is to calculate the probability that a neutral site is polymorphic given local annotations, substitution patterns, and recombination rates. Information is then combined across sites and samples using composite likelihood in order to estimate genome-wide parameters of distinct modes of selection. In addition to parameter estimation, this approach yields a map of the expected neutral diversity levels along the genome. To illustrate the utility of our approach, we apply it to genome-wide resequencing data from 125 lines in Drosophila melanogaster and reliably predict diversity levels at the 1Mb scale. Our results corroborate estimates of a high fraction of beneficial...Continue Reading

References

Sep 3, 1992·Nature·D HouleB Charlesworth
Feb 1, 1974·Genetical Research·J M Smith, J Haigh
Dec 1, 1966·Genetical Research·W G Hill, A Robertson
Jul 19, 1994·Proceedings of the National Academy of Sciences of the United States of America·R R Hudson
Apr 1, 1996·Genetical Research·M NordborgD Charlesworth
Feb 28, 2002·Molecular Biology and Evolution·Bret A Payseur, Michael W Nachman
Mar 5, 2002·Nature·Nick G C Smith, Adam Eyre-Walker
Apr 8, 2003·Molecular Biology and Evolution·Asher D Cutter, Bret A Payseur
Jun 14, 2003·Theoretical Population Biology·Paul Fearnhead
Jul 29, 2004·Genetics·Yuseob Kim, Rasmus Nielsen
Feb 18, 2005·Genetics·Joachim Hermisson, Pleuni S Pennings
May 24, 2005·PLoS Biology·Magnus NordborgJoy Bergelson
Aug 10, 2005·Genome Biology·Penelope R HaddrillPeter Andolfatto
Oct 21, 2005·Nature·Peter Andolfatto
Oct 28, 2005·Genome Research·Rasmus NielsenCarlos Bustamante
Jan 7, 2006·Evolution; International Journal of Organic Evolution·Molly PrzeworskiJeffrey D Wall
Feb 24, 2006·PLoS Biology·Benjamin F VoightJonathan K Pritchard
Mar 8, 2006·Molecular Biology and Evolution·Pleuni S Pennings, Joachim Hermisson
Apr 21, 2006·Genetics·Luis-Miguel Chevin, Frédéric Hospital
Sep 9, 2006·Journal of Mathematical Biology·Carsten Wiuf
Oct 17, 2006·PLoS Genetics·Haipeng Li, Wolfgang Stephan
Dec 19, 2006·PLoS Genetics·Pleuni S Pennings, Joachim Hermisson
Dec 30, 2006·Genetics·Laurence Loewe, Brian Charlesworth
Jul 25, 2007·Molecular Biology and Evolution·Sònia CasillasCasey M Bergman
Jan 17, 2009·PLoS Genetics·James J CaiDmitri A Petrov
May 9, 2009·PLoS Genetics·Graham McVickerPhil Green
Jun 9, 2009·PLoS Genetics·Guy SellaPeter Andolfatto
Jun 9, 2009·PLoS Genetics·Graham CoopJonathan K Pritchard
Sep 10, 2009·Genetics·Paul A Jenkins, Yun S Song
Feb 25, 2010·Current Biology : CB·Jonathan K PritchardGraham Coop
Mar 24, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Wolfgang Stephan
Nov 19, 2010·Journal of the Royal Society, Interface·Harold P de Vladar, Nick H Barton
Feb 19, 2011·Science·Ryan D HernandezMolly Przeworski

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Citations

Sep 24, 2016·Molecular Biology and Evolution·Kasper MunchThomas Mailund
Aug 19, 2016·PLoS Genetics·Emily B Josephs, Stephen I Wright
Nov 1, 2017·BMC Biology·Tom R BookerPeter D Keightley
Aug 9, 2017·Journal of Evolutionary Biology·M RavinetA M Westram
Dec 7, 2017·Genome Biology and Evolution·Felix E G BeaudryStephen I Wright
Nov 9, 2016·PLoS Genetics·Ivan JuricGraham Coop
Dec 6, 2018·Molecular Biology and Evolution·Lex FlagelDaniel R Schrider
Dec 20, 2018·Molecular Ecology Resources·Benjamin C HallerPeter L Ralph
Dec 28, 2018·Molecular Biology and Evolution·Christelle FraïsseBeatriz Vicoso
May 8, 2019·Nature Ecology & Evolution·Lawrence H UricchioDavid Enard
Mar 16, 2019·Genetics·Agnes RettelbachHans Ellegren
Mar 30, 2019·Genetics·José Luis Campos, Brian Charlesworth
Jan 11, 2019·Genetics·Wolfgang Stephan
Nov 8, 2017·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Josep M Comeron
Jul 28, 2019·Molecular Ecology·Remi Matthey-Doret, Michael C Whitlock
Jan 25, 2020·G3 : Genes - Genomes - Genetics·Matthew Hartfield, Thomas Bataillon
Feb 23, 2020·Molecular Biology and Evolution·Jeffrey R AdrionAndrew D Kern
Feb 20, 2020·Genetics·Raul TorresJeffrey Ross-Ibarra
Aug 20, 2020·Proceedings. Biological Sciences·Mohammad A ImritAmro Zayed
Apr 17, 2018·Molecular Biology and Evolution·Brian Charlesworth, Deborah Charlesworth
Jun 14, 2018·Genetics·Himani Sachdeva, Nicholas H Barton
Jun 1, 2017·Proceedings of the National Academy of Sciences of the United States of America·José Luis CamposBrian Charlesworth
Dec 12, 2017·Molecular Biology and Evolution·José Luis CamposBrian Charlesworth
May 31, 2018·Genetics·Ivana CvijovićMichael M Desai
Aug 21, 2020·Proceedings of the National Academy of Sciences of the United States of America·Vince Buffalo, Graham Coop
Oct 3, 2017·PLoS Genetics·Li Zhao, David J Begun
Aug 17, 2018·Molecular Biology and Evolution·August E WoernerMichael F Hammer
Oct 3, 2018·Genetics·Himani Sachdeva, Nicholas H Barton
Dec 15, 2017·Journal of Genetics·Brian Charlesworth
Sep 20, 2019·Ecology and Evolution·Tiina M MattilaTanja Slotte
Jul 21, 2020·Evolutionary Applications·Pierre-Alexandre Gagnaire
Aug 26, 2020·Genetics·Nicolas Galtier, Marjolaine Rousselle
Feb 9, 2021·Evolution Letters·Tom R BookerMichael C Whitlock

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