Pooled whole genome sequencing from year 2004 and Early-Late SNP data from year 2014

Speciation underlies the generation of novel biodiversity. Yet, there is
much to learn about how natural selection shapes genomes during
speciation. Selection is assumed to act against gene flow at barrier loci,
promoting reproductive isolation. However, evidence for gene flow and
selection is often indirect and we know very little about the temporal
stability of barrier loci. Here we utilize haplodiploidy to identify
candidate male barrier loci in hybrids between two wood ant species. As
ant males are haploid they are expected to reveal recessive barrier loci,
which can be masked in diploid females if heterozygous. We then test for
barrier stability in a sample collected ten years later and use survival
analysis to provide a direct measure of natural selection acting on
candidate male barrier loci. We find multiple candidate male barrier loci
scattered throughout the genome. Surprisingly, a proportion of them are
not stable after ten years, natural selection apparently switching from
acting against to favoring introgression in the later sample. Instability
of barrier effect and natural selection for introgressed alleles could be
due to environment-dependent selection, emphasizing the need to consider
temporal variation in the strength of natural selection and the stability
of barrier effect at putative barrier loci in future speciation work.