Estimating effective population size using RADseq: Effects of SNP selection and sample size

Ecology and Evolution
Florianne MarandelVerena M Trenkel

Abstract

Effective population size (Ne ) is a key parameter of population genetics. However, Ne remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site-associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient FIS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Ne estimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data-derived estimates o...Continue Reading

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Citations

Nov 5, 2020·Ecology and Evolution·Elizabeth A MittellBarbara K Mable
Feb 2, 2021·Evolutionary Applications·Elizabeth Carlen, Jason Munshi-South
May 6, 2021·Molecular Ecology Resources·Tin-Yu J HuiAustin Burt
Aug 10, 2021·Ecology and Evolution·Jeronymo DalapicollaGuilherme Oliveira

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Methods Mentioned

BETA
genotyping
PCR

Software Mentioned

R Development Core Team
BWA
NeEstimatorV2
NeEstimator
R
SW
R package whoa

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