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Estimating effective population size from temporal allele frequency changes in experimental evolution

Ágnes Jónás, Thomas Taus, Carolin Kosiol, Christian Schlötterer, Andreas Futschik
doi: https://doi.org/10.1101/051854
Ágnes Jónás
*Vienna Graduate School of Population Genetics, 1210 Wien, Austria
†Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
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Thomas Taus
*Vienna Graduate School of Population Genetics, 1210 Wien, Austria
†Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
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Carolin Kosiol
†Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
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Christian Schlötterer
†Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
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Andreas Futschik
‡Department of Applied Statistics, Johannes Kepler Universität Linz, 4040 Linz, Austria
†Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria
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  • For correspondence: andreas.futschik@jku.at
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Abstract

The effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-Seq). Pool-Seq is cost-effective and outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling increasing the estimated allele frequency variance. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since type I error is accounted for, our method permits the identification of genomic regions that differ significantly in Ne. We present an application to Pool-Seq data from experimental evolution with Drosophila, and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R-package at https://github.com/ThomasTaus/Nest.

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Posted May 05, 2016.
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Estimating effective population size from temporal allele frequency changes in experimental evolution
Ágnes Jónás, Thomas Taus, Carolin Kosiol, Christian Schlötterer, Andreas Futschik
bioRxiv 051854; doi: https://doi.org/10.1101/051854
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Estimating effective population size from temporal allele frequency changes in experimental evolution
Ágnes Jónás, Thomas Taus, Carolin Kosiol, Christian Schlötterer, Andreas Futschik
bioRxiv 051854; doi: https://doi.org/10.1101/051854

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