On the importance of skewed offspring distributions and background selection in virus population genetics

Heredity
K K IrwinJeffrey D Jensen

Abstract

Many features of virus populations make them excellent candidates for population genetic study, including a very high rate of mutation, high levels of nucleotide diversity, exceptionally large census population sizes, and frequent positive selection. However, these attributes also mean that special care must be taken in population genetic inference. For example, highly skewed offspring distributions, frequent and severe population bottleneck events associated with infection and compartmentalization, and strong purifying selection all affect the distribution of genetic variation but are often not taken into account. Here, we draw particular attention to multiple-merger coalescent events and background selection, discuss potential misinference associated with these processes, and highlight potential avenues for better incorporating them into future population genetic analyses.

References

Jun 22, 1995·Proceedings. Biological Sciences·S k Service, S M Blower
Apr 1, 1996·Genetical Research·M NordborgD Charlesworth
Sep 19, 2003·The Journal of General Virology·Elizabeth R ChareEdward C Holmes
Jan 17, 2004·Science·Bryan T GrenfellEdward C Holmes
Jul 20, 2007·Nature Reviews. Genetics·Adam Eyre-Walker, Peter D Keightley
Oct 20, 2007·Genetics·Joanna L DaviesJotun Hein
Nov 7, 2007·BJOG : an International Journal of Obstetrics and Gynaecology·M M CarneiroP M Spritzer
Mar 19, 2008·Journal of Mathematical Biology·Matthias Birkner, Jochen Blath
Jul 1, 2009·Nature Reviews. Genetics·Oliver G Pybus, Andrew Rambaut
May 19, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Rafael Sanjuán
Dec 4, 2010·The Lancet Infectious Diseases·Denis M Tebit, Eric J Arts
Jul 2, 2011·Theoretical Population Biology·Ricky DerJoshua B Plotkin
Jul 5, 2011·Nature Reviews. Microbiology·Etienne Simon-Loriere, Edward C Holmes
Jun 23, 2012·Nature·Kay PrüferSvante Pääbo
Aug 2, 2012·Genetics·Anna-Sapfo MalaspinasMontgomery Slatkin
Aug 2, 2012·Genetics·Natalja Strelkowa, Michael Lässig
Aug 28, 2012·Current Opinion in Virology·Serafín GutiérrezStéphane Blanc
Dec 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Richard A Neher, Oskar Hallatschek
Feb 5, 2013·Theoretical Population Biology·Matthias SteinrückenJochen Blath
Mar 26, 2013·Nature Reviews. Microbiology·Adam S LauringRaul Andino
May 28, 2013·Genetics·Philipp W Messer
Jan 24, 2014·Journal of Virology·Timothy E SchlubMiles P Davenport
Jan 28, 2014·PLoS Genetics·Pleuni S PenningsJohn Wakeley
Mar 4, 2014·PLoS Genetics·Matthieu FollJeffrey D Jensen
Apr 23, 2014·Molecular Ecology·Aurélien Tellier, Christophe Lemaire
Jul 12, 2014·Science·Sarah B Joseph, Ronald Swanstrom
Nov 25, 2014·Genome Biology·Lucy M LiChristophe Fraser
Sep 17, 2015·PLoS Biology·José M CuevasRafael Sanjuán
Sep 24, 2015·Molecular Ecology·Gregory B Ewing, Jeffrey D Jensen
Dec 9, 2015·BMC Evolutionary Biology·Guillermo P Bernet, Santiago F Elena
Dec 15, 2015·Journal of Molecular Biology·Li JiangDaniel N A Bolon
Apr 27, 2016·Theoretical Population Biology·Jochen BlathMatthias Hammer

Citations

Oct 24, 2018·Molecular Biology and Evolution·Dmitry A Filatov
Apr 2, 2020·Evolution; International Journal of Organic Evolution·Ana Y Morales-ArceJeffrey D Jensen
May 13, 2020·Genome Biology and Evolution·Rebecca B Harris, Jeffrey D Jensen
Nov 12, 2017·Genetics·Sebastian MatuszewskiJeffrey D Jensen
Mar 8, 2019·Viruses·Cas RetelPhiline G D Feulner
Feb 3, 2020·Journal of Mathematical Biology·Fabian Freund
Sep 1, 2017·Genome Biology and Evolution·Louise OrmondJennifer P Wang
Oct 17, 2019·Science Advances·Cas RetelPhiline G D Feulner
Jul 16, 2020·Molecular Biology and Evolution·F MenardoFabian Freund
Sep 2, 2020·Annual Review of Genetics·Bjarki Eldon

Related Concepts

Biological Evolution
Genetics, Population
Genetic Linkage Analysis
Selection, Genetic
Zoophaginae
Nucleotides
Health Care
Size
Inference
Adverse Event

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