Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

Restriction site-associated DNA sequencing (RAD-seq) provides high-resolution population genomic data at low cost, and has become an important component in ecological and evolutionary studies. As with all high-throughput technologies, analytic strategies require critical validation to ensure accurate and unbiased interpretation.
To test for the impact of bioinformatic data processing on downstream population genetic inferences, we analysed mammalian RAD-seq data (>100 individuals) with 312 combinations of methodology (de novo vs. mapping to references of increasing divergence) and filtering criteria (missing data, HWE, FIS, coverage, mapping, genotype quality). In an effort to identify commonalities and biases in all pipelines, we computed summary statistics (nr. loci, nr. SNP, π, Hetobs, FIS, FST, Ne, m) and compared the results to independent null expectations (isolation-by-distance correlation, expected transition-to-transversion ratio Ts/Tv, Mendelian mismatch rates of known par...