Detecting genetic signals of selection in heavily bottlenecked reindeer populations by comparing parallel founder events

Founder populations are of special interest to both evolutionary and
conservation biologists, but the detection of genetic signals of selection
in these populations is challenging due to their demographic history.
Geographically separated founder populations likely subjected to similar
selection pressures provide an ideal but rare opportunity to overcome
these challenges. Here we take advantage of such a situation generated
when small, isolated founder populations of reindeer were established on
the island of South Georgia, and using this system we look for empirical
evidence of selection overcoming strong genetic drift. We generated a 70K
ddRADseq SNP database for the two parallel reindeer founder populations
and screened for signatures of soft sweeps. We find evidence for a genomic
region under selection shared among the two populations, and support our
findings with Wright-Fisher model simulations to assess the power and
specificity of interpopulation selection scans – i.e. Bayescan, OutFLANK,
PCadapt and a newly developed scan called Genome Wide Differentiation Scan
(GWDS) – in the context of pairwise source-founder comparisons. Our
simulations indicate that loci under selection in small founder
populations are most likely detected by GWDS, and strengthen the
hypothesis that the outlier region represents a true locus under
selection. We explore possible, relevant functional roles for genes in
linkage with the detected outlier locus.