Data from: Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences

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.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 explanation