The site frequency/dosage spectrum of autopolyploid populations
Ferretti, Luca (The Pirbright Institute (Regne Unit))
Ribeca, Paolo (The Pirbright Institute (Regne Unit))
Ramos-Onsins, Sebastian (Centre de Recerca en Agrigenòmica)

Date:	2018
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.
Grants:	Ministerio de Educación y Ciencia AGL2016-78709-R Ministerio de Economía y Competitividad SEV-2015-0533
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Subject:	Autopolyploidy ; Dosage distribution ; Hardy-Weinberg equilibrium ; High-throughput sequencing ; Site frequency ; Neutrality tests ; Allelic dosage
Published in:	Frontiers in genetics, Vol. 9 (Oct. 2018) , art. 480, ISSN 1664-8021

DOI: 10.3389/fgene.2018.00480
PMID: 30405691

13 p, 1.4 MB

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Research literature > UAB research groups literature > Research Centres and Groups (research output) > Experimental sciences > CRAG (Centre for Research in Agricultural Genomics)
Articles > Research articles
Articles > Published articles