Data from: Developing reduced SNP assays from whole-genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

The most important managed pollinator, the honeybee (Apis mellifera L.),
has been subject to a growing number of threats. In Western Europe one
such threat is large-scale introductions of commercial strains (C-lineage
ancestry), which is leading to introgressive hybridization and even the
local extinction of native honeybee populations (M-lineage ancestry).
Here, we developed reduced assays of highly informative SNPs from 176
whole genomes to estimate C-lineage introgression in the most diverse and
evolutionarily complex subspecies in Europe, the Iberian honeybee (Apis
mellifera iberiensis). We started by evaluating the effects of sample size
and sampling a geographically restricted area on the number of highly
informative SNPs. We demonstrated that a bias in the number of fixed SNPs
(FST=1) is introduced when the sample size is small (N≤10) and when
sampling only captures a small fraction of a population’s genetic
diversity. These results underscore the importance of having a
representative sample when developing reliable reduced SNP assays for
organisms with complex genetic patterns. We used a training dataset to
design four independent SNP assays selected from pairwise FST between the
Iberian and C-lineage honeybees. The designed assays, which were validated
in holdout and simulated hybrid datasets, proved to be highly accurate and
can be readily used for monitoring populations not only in the native
range of A. m. iberiensis in Iberia but also in the introduced range in
the Balearic islands, Macaronesia, and South America, in a time- and
cost-effective manner. While our approach used the Iberian honeybee as
model system, it has a high value in a wide range of scenarios for the
monitoring and conservation of potentially hybridized domestic and
wildlife populations.