DOI: 10.5061/dryad.jf361
title: Data from: Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences

description: There is a lack of consensus on how next-generation sequence data should
 be considered for phylogenetic and phylogeographic estimates, with some
 studies excluding loci with missing data, while others include them, even
 when sequences are missing from a large number of individuals. Here we use
 simulations, focusing specifically on RAD sequences, to highlight some of
 the unforeseen consequence of excluding missing data from next-generation
 sequencing. Specifically, we show that in addition to the obvious effects
 associated with reducing the amount of data used to make historical
 inferences, the decisions we make about missing data (such as the minimum
 number of individuals with a sequence for a locus to be included in the
 study) also impact the types of loci sampled for a study. In particular,
 as the tolerance for missing data becomes more stringent, the mutational
 spectrum represented in the sampled loci becomes truncated such that loci
 with the highest mutation rates are disproportionately excluded. This
 effect is exacerbated further by factors involved in the preparation of
 the genomic library (i.e., the use of reduced representation libraries, as
 well as the coverage) and the taxonomic diversity represented in the
 library (i.e., the level of divergence among the individuals). We
 demonstrate that the intuitive appeals about being conservative by
 removing loci may be misguided.
description: speciestree20 species tree simulated under Yule model using MesquitemsPerl script to simulate coalescent genealogies for given species treeseqgene_paramtershort R script to generate random mutation rates (as the theta for simulating dna sequences ) from a log normal distributionseqgen parametersthe result from seqgene_paramter.R-- the mutation rates used in simulating sequencesseqge.parameterseq-genPerl script to simulate sequences given genealogies and mutation rate (as theta)infomissinga Perl script to filter out sequences with mutations at enzyme cutting sitescoveragea Perl script for filtering out sequences with no read (coverage draw from a poisson distribution)clustera Perl script for generating post-sequencing missing datalociinda perl script for summarizing the number of individuals for each locus (output in a txt file)countsa Perl script for counting the number loci at different tolerance levels (output a txt file)phylipranda Perl script for generating phylip formatted sequence files with two tolerance levels (as the number of minimal individuals)--one for specifying the number of loci, and one for specifying the mutation-rate spectrummonosp_dryadR code for calculating the number of monophyletic clades on estimated gene treemindisR script for shallowest divergenece species tree estimationtreedistR script for calculating RF distanceraxmlrun raxmlGenealogy.tarSimulated genalogiesCompleteSequenceData.tarSimulated complete sequence dataCuttingMissing.tarremaining sequences after filtering out sequences with mutations at enzyme cutting sitesCoverageMissing.tarremaining data after filtering sequences with zero read, mean coverage set to 5xCoverageOneMissing.tarRemaining data after filtering out sequences with no read, mean coverage set to 1xDataProcessingMissing.tarremaining data after data processing steps, mean coverage 5xDataProcessingOneMissing.tarRemaining sequences after data processing step, mean coverage 1xDryadfilelistFile list and explanations