Data from: Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird

Information on genetic relationships among individuals is essential to
many studies of the behavior and ecology of wild organisms. Parentage and
relatedness assays based on large numbers of SNP loci hold substantial
advantages over the microsatellite markers traditionally used for these
purposes. We present a double-digest restriction site-associated DNA
sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously
achieves the SNP discovery and genotyping steps and which is optimized to
return a statistically powerful set of SNP markers (typically 150-600
after stringent filtering) from large numbers of individuals (up to 240
per run). We explore the tradeoffs inherent in this approach through a set
of experiments in a species with a complex social system, the variegated
fairy-wren (Malurus lamberti), and further validate it in a
phylogenetically broad set of other bird species. Through direct
comparisons with a parallel dataset from a robust panel of highly variable
microsatellite markers, we show that this ddRAD-seq approach results in
substantially improved power to discriminate among potential relatives and
considerably more precise estimates of relatedness coefficients. The
pipeline is designed to be universally applicable to all bird species (and
with minor modifications to many other taxa), to be cost- and
time-efficient, and to be replicable across independent runs such that
genotype data from different study periods can be combined and analyzed as
field samples are accumulated.