Gene-flow in a mosaic hybrid zone: is local

20 Genomewide scans of genetic differentiation between hybridizing taxa can identify genome 21 regions with unusual rates of introgression. Regions of high differentiation might repre22 sent barriers to gene flow, while regions of low differentiation might indicate adaptive intro23 gression the spread of selectively beneficial alleles between reproductively isolated genetic 24 backgrounds. Here we conduct a scan for unusual patterns of differentiation in a mosaic 25 hybrid zone between two mussel species, Mytilus edulis and Mytilus galloprovincialis. One 26 outlying locus, mac-1, showed a characteristic footprint of local introgression, with abnor27 mally high frequency of edulis-derived alleles in a patch of M. galloprovincialis enclosed 28 within the mosaic zone, but low frequencies outside of the zone. Further analysis of DNA 29 sequences showed that almost all of the edulis allelic diversity had introgressed into the M. 30 galloprovincialis background in this patch. We then used a variety of approaches to test the 31 hypothesis that there had been adaptive introgression at mac-1. Simulations and model fitting 32 with Maximum Likelihood and Approximate Bayesian Computation approaches suggested 33 that adaptive introgression could generate a “soft sweep”, which was qualitatively consis34 tent with our data. Although the migration rate required was high, it was compatible with 35 the functioning of an effective barrier to gene flow as revealed by demographic inferences. 36 As such, adaptive introgression could explain both the reduced intraspecific differentiation 37 around mac-1 and the high diversity of introgressed alleles, although a localised change in 38 barrier strength may also be invoked. Together, our results emphasize the need to account for 39 the complex history of secondary contacts in interpreting outlier loci. 40