DOI: 10.5061/dryad.4vr8kp3
title: Data from: How “simple” methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish

description: Reduced representation (RRL) sequencing approaches (e.g., RADSeq,
 genotyping by sequencing) require decisions about how much to invest in
 genome coverage and sequencing depth (library quality), as well as choices
 of values for adjustable bioinformatics parameters. To empirically explore
 the importance of these “simple” decisions, we generated two independent
 sequencing libraries for the same 142 individual lake whitefish (Coregonus
 clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and
 low sequencing depth (library A); and (2) more loci and higher sequencing
 depth (library B). The fish were selected from populations with different
 levels of expected genetic subdivision. Each library was analyzed using
 the STACKS pipeline followed by three types of population structure
 assessment (FST, DAPC and ADMIXTURE) with iterative increases in the
 stringency of sequencing depth and missing data requirements, as well as
 more specific a priori population maps. Library B was always able to
 resolve strong population differentiation in all three types of assessment
 regardless of the selected parameters. In contrast, library A produced
 more variable results; increasing the minimum sequencing depth threshold
 (-m) resulted in a reduced number of retained loci, and therefore lost
 resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and
 DAPC were robust to varying the population map and increasing the
 stringency of missing data requirements. In contrast, ADMIXTURE was unable
 to resolve strong population differentiation when increasing these same
 parameters in library A. Similarly, when examining fine scale population
 subdivision, library B was robust to changing parameters but library A
 lost resolution depending on the parameter set. We used library B to
 examine actual subdivision in our study populations. All three types of
 analysis found complete subdivision among populations in Lake Huron, ON
 and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population
 subdivision was detected in Lake Huron with fish from sites in the
 north-west, Search Bay, North Point and Hammond Bay, showing slight
 differentiation. Overall, we show that apparently simple decisions about
 library quality and bioinformatics parameters can have potentially
 important impacts on the interpretation of population subdivision.
 Although costly, the early investment in a high-quality library and more
 conservative stringency settings on STACKS parameters lead to a final
 dataset that was more consistent and robust when examining both weak and
 strong population differentiation.
description: 9merDatav1.tarnextRAD 9mer data sequenced using Illumina HiSeq 4000 data9merDatav2nextRAD 9mer data sequenced using Illumina HiSeq 4000 data9merDatav3nextRAD 9mer data sequenced using Illumina HiSeq 4000 data10merDatav1nextRAD 10mer data sequenced using Illumina HiSeq 4000 data10merDatav2nextRAD 10mer data sequenced using Illumina HiSeq 4000 data10merDatav3nextRAD 10mer data sequenced using Illumina HiSeq 4000 dataSampleInfoSample info for each sequencing library