RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

Reduced representation genome-sequencing approaches based on restriction digestion are enabling large-scale marker generation and facilitating genomic studies in a wide range of model and nonmodel systems. However, sampling chromosomes based on restriction digestion may introduce a bias in allele frequency estimation due to polymorphisms in restriction sites. To explore the effects of this nonrandom sampling and its sensitivity to different evolutionary parameters, we developed a coalescent-simulation framework to mimic the biased recovery of chromosomes in restriction-based short-read sequencing experiments (RADseq). We analysed simulated DNA sequence datasets and compared known values from simulations with those that would be estimated using a RADseq approach from the same samples. We compare these ‘true’ and ‘estimated’ values of commonly used summary statistics, π, θw, Tajima's D and FST. We show that loci with missing haplotypes have estimated summary statistic values that can devi...