The Site Frequency/Dosage Spectrum of Autopolyploid Populations

Frontiers in Genetics
Luca FerrettiSebástian E Ramos-Onsins

Abstract

The Site Frequency Spectrum (SFS) and the heterozygosity of allelic variants are among the most important summary statistics for population genetic analysis of diploid organisms. We discuss the generalization of these statistics to populations of autopolyploid organisms in terms of the joint Site Frequency/Dosage Spectrum and its expected value for autopolyploid populations that follow the standard neutral model. Based on these results, we present estimators of nucleotide variability from High-Throughput Sequencing (HTS) data of autopolyploids and discuss potential issues related to sequencing errors and variant calling. We use these estimators to generalize Tajima's D and other SFS-based neutrality tests to HTS data from autopolyploid organisms. Finally, we discuss how these approaches fail when the number of individuals is small. In fact, in autopolyploids there are many possible deviations from the Hardy-Weinberg equilibrium, each reflected in a different shape of the individual dosage distribution. The SFS from small samples is often dominated by the shape of these deviations of the dosage distribution from its Hardy-Weinberg expectations.

References

Apr 1, 1975·Theoretical Population Biology·G A Watterson
Oct 1, 1995·Theoretical Population Biology·Y X Fu
May 24, 2000·Proceedings of the National Academy of Sciences of the United States of America·D V Butruille, L S Boiteux
Nov 26, 2002·Molecular Biology and Evolution·Sebástian E Ramos-Onsins, Julio Rozas
Nov 25, 2004·Theoretical Population Biology·Noah A Rosenberg, Peter P Calabrese
Nov 11, 2005·Molecular Biology and Evolution·Michael Lynch
Nov 16, 2005·Annual Review of Genetics·Rasmus Nielsen
Jun 20, 2008·Genetics·Guillaume Achaz
Feb 25, 2009·Molecular Ecology·Lou Jost
Jan 15, 2010·The New Phytologist·Christian ParisodChristian Brochmann
Jul 9, 2010·Genetics·Luca FerrettiSebástian E Ramos-Onsins
Mar 25, 2011·Molecular Ecology Resources·Patrick G Meirmans, Philip W Hedrick
Jan 10, 2012·Proceedings of the National Academy of Sciences of the United States of America·Michael ChesterDouglas E Soltis
Jun 5, 2012·Genetics·Luca FerrettiSebástian E Ramos-Onsins
Jun 21, 2012·Genetics·B ArnoldJ Wakeley
Sep 21, 2012·BMC Bioinformatics·Emanuele RaineriMiguel Pérez-Enciso
Dec 6, 2012·Heredity·Patrick G Meirmans, Peter H van Tienderen
Jan 4, 2013·PLoS Genetics·Jesse D HollisterKirsten Bomblies
Oct 10, 2013·Molecular Ecology·Luca FerrettiMiguel Pérez-Enciso
Jan 18, 2015·Theoretical Population Biology·Luca Ferretti, Sebástian E Ramos-Onsins
Jun 10, 2015·Journal of Applied Genetics·M Mielczarek, J Szyda
Oct 7, 2015·The New Phytologist·Michael S BarkerDonald A Levin
Nov 27, 2015·Molecular Ecology Resources·Paul D BlischakAndrea D Wolfe
Jan 18, 2017·Proceedings of the National Academy of Sciences of the United States of America·Ksenia V KrasilevaJorge Dubcovsky
Jan 22, 2017·G3 : Genes - Genomes - Genetics·Takahiro Maruki, Michael Lynch
Mar 9, 2017·Genetics·Sònia Casillas, Antonio Barbadilla
Apr 8, 2017·The Plant Journal : for Cell and Molecular Biology·Artem S KasianovAleksey A Penin
Oct 12, 2017·Nature·Jay ShendureRobert H Waterston
Feb 1, 2018·The Journal of Heredity·Patrick G MeirmansPeter H van Tienderen

Citations

Jan 23, 2021·Molecular Ecology Resources·Vivaswat ShastryC Alex Buerkle

Related Concepts

Nucleotides
Site
Shapes
Gene Mutant
Analysis
Diploid Cell
Nucleic Acid Sequencing
Joint by Site
High-Throughput RNA Sequencing

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