Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa.

Nature Ecology & Evolution
Patrick MonnahanLevi Yant

Abstract

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical data remains sparse. We sequenced ~300 individuals from 39 populations of Arabidopsis arenosa, a naturally diploid-autotetraploid species. We find that the impacts of polyploidy on population genomic processes are subtle yet pervasive, such as reduced efficiency of purifying selection, differences in linked selection and rampant gene flow from diploids. Initial masking of deleterious mutations, faster rates of nucleotide substitution and interploidy introgression likely conspire to shape the evolutionary potential of polyploids.

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Citations

Feb 26, 2020·Biology Letters·Patrick Monnahan, Yaniv Brandvain
Sep 26, 2020·American Journal of Botany·Emma J MorganFilip Kolář
Nov 20, 2019·Nature Communications·Sarah MarburgerLevi Yant
Aug 28, 2020·Frontiers in Genetics·Gonzalo Nieto FelinerJonathan F Wendel
Apr 11, 2020·Proceedings of the National Academy of Sciences of the United States of America·Chris MorganKirsten Bomblies
Dec 29, 2020·Frontiers in Plant Science·Adam KnotekFilip Kolář
Dec 2, 2020·The Plant Journal : for Cell and Molecular Biology·Guillaume WosFilip Kolář
Jan 23, 2021·Molecular Ecology Resources·Vivaswat ShastryC Alex Buerkle
Nov 19, 2020·Proceedings. Biological Sciences·Kirsten Bomblies
Jan 28, 2021·Molecular Biology and Evolution·Magdalena BohutínskáPirita Paajanen
Jan 31, 2021·Journal of Hazardous Materials·Żaneta GierońEugeniusz Małkowski
Jan 18, 2021·The New Phytologist·Roswitha Schmickl, Levi Yant
May 19, 2021·Proceedings of the National Academy of Sciences of the United States of America·Magdalena BohutínskáFilip Kolář
Jul 13, 2021·Evolution; International Journal of Organic Evolution·Jonathan P SpoelhofPamela S Soltis
Mar 31, 2021·Molecular Biology and Evolution·Magdalena BohutínskáLevi Yant
Aug 21, 2021·Molecular Ecology Resources·Stefan WötzelFelix Gugerli

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Methods Mentioned

BETA
RNAseq

Software Mentioned

bwa
bcftools
phyml
Qubit
SplitsTree
picard
R
HaplotypeCaller
msprime
fastsimcoal

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