Data from: Applicability of RAD-tag genotyping for inter-familial comparisons: empirical data from two cetaceans

Restriction site-Associated DNA tag (RAD-tag) sequencing has become a
popular approach to generate thousands of SNPs used to address diverse
questions in population genomics. Comparatively, the suitability of
RAD-tag genotyping to address evolutionary questions across divergent
species has been the subject of only a few recent studies. Here, we
evaluate the applicability of this approach to conduct genome-wide scans
for polymorphisms across two cetacean species belonging to distinct
families: the short-beaked common dolphin (Delphinus delphis; n = 5
individuals) and the harbor porpoise (Phocoena phocoena; n = 1
individual). Additionally, we explore the effects of varying two
parameters in the Stacks analysis pipeline on the number of loci and level
of divergence obtained. We observed a 34% drop in the total number of loci
that were present in all individuals when analyzing individuals from the
distinct families compared to analyses restricted to intra-specific
comparisons (i.e., within D. delphis). Despite relatively stringent
quality filters, 3,595 polymorphic loci were retrieved from our
inter-familial comparison. Cetaceans have undergone rapid diversification
and the estimated divergence time between the two families is relatively
recent (14 to 19 My). Thus, our results showed that, for this level of
divergence, a large number of orthologous loci can still be genotyped
using this approach, which is on par with two recent in silico studies.
Our findings constitute one of the first empirical investigations using
RAD-tag sequencing at this level of divergence and highlights the great
potential of this approach in comparative studies and to address
evolutionary questions.