Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish

Evolution Letters
Quiterie HaenelDaniel Berner

Abstract

Genomic studies of parallel (or convergent) evolution often compare multiple populations diverged into two ecologically different habitats to search for loci repeatedly involved in adaptation. Because the shared ancestor of these populations is generally unavailable, the source of the alleles at adaptation loci, and the direction in which their frequencies were shifted during evolution, remain elusive. To shed light on these issues, we here use multiple populations of threespine stickleback fish adapted to two different types of derived freshwater habitats-basic and acidic lakes on the island of North Uist, Outer Hebrides, Scotland-and the present-day proxy of their marine ancestor. In a first step, we combine genome-wide pooled sequencing and targeted individual-level sequencing to demonstrate that ecological and phenotypic parallelism in basic-acidic divergence is reflected by genomic parallelism in dozens of genome regions. Exploiting data from the ancestor, we next show that the acidic populations, residing in ecologically more extreme derived habitats, have adapted by accumulating alleles rare in the ancestor, whereas the basic populations have retained alleles common in the ancestor. Genomic responses to selection are thu...Continue Reading

References

Mar 20, 2001·American Journal of Human Genetics·M StephensP Donnelly
Apr 8, 2004·Proceedings of the National Academy of Sciences of the United States of America·William A CreskoJohn H Postlethwait
Jul 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Kazuhiko KawasakiKenneth M Weiss
Feb 18, 2005·Genetics·Joachim Hermisson, Pleuni S Pennings
Nov 21, 2007·Trends in Ecology & Evolution·Jeff Arendt, David Reznick
Oct 15, 2008·PloS One·Nathan A BairdEric A Johnson
Mar 4, 2009·Development Genes and Evolution·Kazuhiko Kawasaki
Dec 21, 2010·Bioinformatics·Klaus Peter Schliep
Feb 16, 2012·Molecular Ecology·Valérie Le Corre, Antoine Kremer
Apr 7, 2012·Nature·Felicity C JonesDavid M Kingsley
Jun 26, 2012·BMC Evolutionary Biology·Marius RoestiDaniel Berner
Dec 15, 2012·The Journal of Animal Ecology·Andrew D C MacCollJob de Roij
Apr 23, 2013·Molecular Ecology·Marius RoestiDaniel Berner
Jun 22, 2013·Ecology and Evolution·Rowena SpenceCarl Smith
Sep 21, 2013·Genome Research·Simon H MartinChris D Jiggins
Oct 1, 2013·Trends in Ecology & Evolution·Philipp W Messer, Dmitri A Petrov
Mar 19, 2014·Molecular Ecology·Marius RoestiDaniel Berner
Aug 12, 2015·Trends in Genetics : TIG·Daniel Berner, Walter Salzburger
Dec 15, 2015·Bioinformatics·Michael Matschiner
Dec 17, 2015·Nature Communications·Marius RoestiDaniel Berner
Dec 17, 2015·Proceedings of the National Academy of Sciences of the United States of America·Emily A LescakWilliam A Cresko
Jul 5, 2016·Molecular Ecology·Isabel S MagalhaesAndrew D C MacColl
Aug 12, 2016·Proceedings. Biological Sciences·Aliya El Nagar, Andrew D C MacColl
Oct 7, 2016·Science·Sam YeamanSally N Aitken
Jun 21, 2017·Science Advances·Tore O ElgvinGlenn-Peter Sætre
Oct 11, 2017·Molecular Ecology·Daniel Berner, Marius Roesti

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Citations

Aug 14, 2019·Genome Biology and Evolution·Nadezhda V TerekhanovaNikolai S Mugue
Apr 2, 2020·Genome Biology and Evolution·Kohta YoshidaJun Kitano
Jul 11, 2019·Evolution Letters·Ken A ThompsonDolph Schluter
Dec 12, 2020·IScience·M Lisette Delgado, Daniel E Ruzzante
Nov 18, 2020·Journal of Evolutionary Biology·Juliane HartkeBarbara Feldmeyer
Jan 28, 2021·Molecular Biology and Evolution·Magdalena BohutínskáPirita Paajanen
May 19, 2021·Proceedings of the National Academy of Sciences of the United States of America·Magdalena BohutínskáFilip Kolář
Jun 20, 2021·Journal of Evolutionary Biology·Carmelo FrucianoJulia C Jones
Jun 17, 2021·Molecular Ecology·Jonathan M Waters, Graham A McCulloch
Oct 1, 2021·Molecular Ecology·Graham A McCullochJonathan M Waters

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Methods Mentioned

BETA
PCR

Software Mentioned

R Core Team
R package phangorn
BayPass
Geneious
R
Rsamtools
RAxML
Dryad
FITCHI
PHASE

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