Patterns of introgression in farmed mussels: A genomic study of Mytilus spp. in northern Scotland and Ireland

Understanding genetic diversity and gene flow, both within and between mussel populations, can inform population fitness and support sustainable aquaculture. While hybrid zones occur naturally across the Mytilus species complex's distribution, human activities and aquaculture practices can also bring genetically distinct mussel lineages into contact, promoting hybridisation. When these interactions occur across multiple locations, they offer insights into admixture, local adaptation, and their implications for aquaculture. We analysed the genetic structure of rope-grown Mytilus mussels from key sites along the Scottish and Irish coasts. A total of 204 individuals were genotyped using a medium-density multi-species SNP array. Samples included mussels from western Ireland and six Scottish sites: two from Shetland, one from Cromarty Firth, one from the Western Isles and one from the Aberdeen marine monument. Reference samples of M. edulis, M. galloprovincialis, and M. trossulus were included to assess hybridisation and introgression. Most populations showed predominant M. edulis ancestry with 10–25% M. galloprovincialis introgression, except Cromarty, where no introgression was detected. Mussels from Shetland, the Western Isles, and Ireland were more closely related, each showing varying levels of M. galloprovincialis ancestry. A distinct pattern was observed in Aberdeen, with individuals carrying ∼50% M. galloprovincialis ancestry, pointing to extensive admixture within a hybrid zone. Local and shared introgressed genomic regions were identified using ancestry inference software, ELAI, including signals of potential adaptive introgression. These findings highlight the complex ancestry and spatial genetic structure of Mytilus populations in the North Atlantic and demonstrate the utility of SNP arrays and reference data to inform site selection, spat source management, and aquaculture resilience under changing environmental and genetic conditions.