DOI: 10.5061/dryad.xsj3tx9d9
title: Pre-introduction introgression contributes to parallel differentiation and contrasting hybridisation outcomes between invasive and native marine mussels

description: Non-native species experience novel selection pressures in introduced
 environments and may interbreed with native
 lineages. Species introductions therefore provide opportunities
 to investigate repeated patterns of adaptation and introgression across
 replicated contact zones. Here, we investigate genetic
 parallelism between multiple introduced populations of the invasive marine
 mussel, Mytilus galloprovincialis, in the absence (South Africa
 and California) and presence of hybridisation with a native congener
 (Mytilus planulatus in Batemans Bay and Sydney Harbour,
 Australia). Repeatability in post-introduction differentiation
 from native-range populations varied between genetically distinct Atlantic
 and Mediterranean lineages, with Atlantic-derived introductions displaying
 high differentiation (maxFST&gt;0.4) and parallelism at outlier loci.
 Identification of long non-coding RNA transcripts
 (lncRNA) additionally allowed us to clarify
 that parallel responses are largely limited to protein-coding
 loci, with lncRNAs likely evolving under evolutionary
 constraints. Comparisons of independent hybrid zones
 revealed differential introgression most strongly in Batemans
 Bay, with an excess of M. galloprovincialis ancestry and
 resistance to introgression at loci differentiating parental lineages (M.
 planulatus and Atlantic M.
 galloprovincialis). Additionally, contigs putatively
 introgressed with divergent alleles from a closely related
 species, Mytilus edulis, showed stronger introgression
 asymmetries compared to genome-wide trends and also diverged in parallel
 in both Atlantic-derived introductions. These results suggest that
 divergent demographic histories experienced by introduced lineages,
 including pre-introduction introgression, influences contemporary
 admixture dynamics. Our findings build on previous investigations
 reporting contributions of historical introgression to
 intrinsic reproductive architectures shared
 between marine lineages and illustrate that interspecific
 introgression history can shape differentiation between
 colonising populations and their hybridisation with
 native congeners.
description: ReferenceTranscriptome_Files: 1) Mytilus
 galloprovincialis de novo transcriptome 'total' assembly,
 containing 143,093 nuclear sequences. This file was used as a reference
 assembly for variant discovery and as input for downstream genomic
 analyses of parallelism and introgression. 2) Mytilus
 galloprovincialis de novo transcriptome 'full' assembly,
 containing 106,333 nuclear sequences, with all putative lncRNA trascripts
 removed. This file was used as a reference assembly for variant discovery
 and as input for downstream population genomic analyses of population
 differentiation. 3) Mytilus galloprovincialis de novo
 transcriptome 'lncRNA' assembly, containing 44,096 putative
 lncRNA transcripts. This file was used as a reference assembly for variant
 discovery and as input for downstream population genomic analyses of
 population differentiation.
 FilteredVCF_Files_PopGenomicAnalyses: 1-3)
 Filtered VCF files derived from the 'total' assembly used for
 input for downstream genomic analyses of parallelism and
 introgression. 4-5) Filtered VCF files derived from the
 'full' and 'lncRNA' assemblies used for input
 for downstream genomic analyses of population genomic differentiation and
 lncRNA evolution.