Population genomics from pool sequencing. Issue 22 (28th October 2013)

• Record Type: Journal Article
• Authors: Ferretti, Luca; Ramos‐Onsins, Sebastián E.; Pérez‐Enciso, Miguel
• Is Part Of: Molecular ecology. Volume 22:Issue 22(2013)
• Page Start: 5561
• Page End: 5576
• Publication Date: 2013-10-28
• Subjects: composite likelihood estimators -- genetic differentiation -- high‐throughput sequencing -- neutrality tests -- pool sequencing; Molecular ecology -- Periodicals; Molecular population biology -- Periodicals; 576
• DOI: 10.1111/mec.12522
• Languages: English
• ISSNs: 0962-1083

Abstract

Abstract: Next generation sequencing of pooled samples is an effective approach for studies of variability and differentiation in populations. In this paper we provide a comprehensive set of estimators of the most common statistics in population genetics based on the frequency spectrum, namely the Watterson estimator θ W, nucleotide pairwise diversity Π, Tajima's D, Fu and Li's D and F, Fay and Wu's H, McDonald‐Kreitman and HKA tests and F ST, corrected for sequencing errors and ascertainment bias. In a simulation study, we show that pool and individual θ estimates are highly correlated and discuss how the performance of the statistics vary with read depth and sample size in different evolutionary scenarios. As an application, we reanalyse sequences from Drosophila mauritiana and from an evolution experiment in Drosophila melanogaster . These methods are useful for population genetic projects with limited budget, study of communities of individuals that are hard to isolate, or autopolyploid species.