Genotype-free estimation of allele frequencies from RADSeq data in pied flycatchers

We compare two methods of allele frequency estimation from RADSeq data for demographic inference using three populations of pied flycatchers for which resequencing data are available (NCBI BIOPROJECT:PRJEB7359; https://www.ncbi.nlm.nih.gov/bioproject/266403). We show that demographic parameter estimates from RADSeq data fall within the 95% confidence interval of those produced from resequencing data when allele frequencies are estimated using genotype-free methods but can deviate strongly from re-sequencing data when genotype-based methods are used.